Evolutionary Classification of CRISPR‐Cas Systems

Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

doi:10.1002/9781683673798.ch2

Cited by 15 publications

(13 citation statements)

References 138 publications

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“…The maturation and conversion of pre-crRNA to crRNAs is accomplished by a specific RNA endonuclease complicated or by an alternating mechanism involving bacterial RNase III. The maturing crRNA binds with the Cas protein targeting cognate DNA or RNA (Makarova and Koonin, 2015).…”

Section: Genome Editing Tool Crispr/cas9 Systemmentioning

confidence: 99%

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CRISPR/Cas9 Systems and Gene Editing Technology

Gök

Beyaz

Aslan

2023

Osmaniye Korkut Ata Üniversitesi Fen Bilimleri Enstitüsü Dergisi

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This review on gene editing technologies summarizes the features, applications and future of the CRISPR/Cas9 genome regulating system. Recently, the aim of searchers has been to improve cost-effective and reliable ways to perform goal modify to the genome of living cells. Thanks to the improvement of the CRISPR/Cas9 system, it has made progress in many fields such as molecular biology, biomedicine and medicine. Moreover, it has contributed to important developments in the field of genome engineering through targeted breaks in the DNA of almost every organism and cell type.

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Section: Genome Editing Tool Crispr/cas9 Systemmentioning

confidence: 99%

“…Cas3, Cas9 and Cas10 are special to type I, type II and type III CRISPR/Cas systems, respectively. All of them contain components necessary for the basic steps of the defensive mechanism (Makarova and Koonin, 2015;Gupta et al, 2019). CRISPR/Cas9 contains two components for DNA cleavage.…”

Section: Genome Editing Tool Crispr/cas9 Systemmentioning

confidence: 99%

CRISPR/Cas9 Systems and Gene Editing Technology

Gök

Beyaz

Aslan

2023

Osmaniye Korkut Ata Üniversitesi Fen Bilimleri Enstitüsü Dergisi

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“…Class 1 CRISPR−Cas systems employ complexes of multiple effector proteins and include 3 main types (I, III, and IV), whereas class 2 CRISPR−Cas systems utilize one protein effector and consist of 3 main types (II, V, and VI) and 17 subtypes. 83,123 Class 1 systems widely exist, constituting up to half of the CRISPR−Cas loci in archaea and bacteria. In contrast, class 2 systems represent ∼10% of the CRISPR−Cas loci found in bacteria but are virtually not present in archaea.…”

Section: Crispr−cas Systemsmentioning

confidence: 99%

New Insights for Biosensing: Lessons from Microbial Defense Systems

Wan

Zong

et al. 2022

Chem. Rev.

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Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR−Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR−Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties.We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.

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“…Among the most widely studied are CRISPR-Cas systems found in diverse bacteria and archaea (1). CRISPR-Cas systems typically include an RNA-guided nuclease (effector) complex, a CRISPR repeat locus that accepts snippets of nucleic acids (protospacers) derived from threats, enzymes (Cas4, Cas5, or Cas6) that process transcribed spacers into RNA guides for nuclease effector complexes, and a DNA integrase (Cas1/Cas2) that site-specifically integrates new spacers from invading pathogens into CRISPR arrays (2)(3)(4)(5)(6)(7)(8). Six types of CRISPR systems (types I to VI) each with multiple subclasses have been distinguished (1).…”

Section: Introductionmentioning

confidence: 99%

Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase–Cas1 fusion protein

Mohr,

Yao,

Park

et al. 2024

Sci. Adv.

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Reverse transcriptase–Cas1 (RT-Cas1) fusion proteins found in some CRISPR systems enable spacer acquisition from both RNA and DNA, but the mechanism of RNA spacer acquisition has remained unclear. Here, we found that Marinomonas mediterranea RT-Cas1/Cas2 adds short 3′-DNA (dN) tails to RNA protospacers, enabling their direct integration into CRISPR arrays as 3′-dN-RNAs or 3′-dN-RNA/cDNA duplexes at rates comparable to similarly configured DNAs. Reverse transcription of RNA protospacers is initiated at 3′ proximal sites by multiple mechanisms, including recently described de novo initiation, protein priming with any dNTP, and use of short exogenous or synthesized DNA oligomer primers, enabling synthesis of near full-length cDNAs of diverse RNAs without fixed sequence requirements. The integration of 3′-dN-RNAs or single-stranded DNAs (ssDNAs) is favored over duplexes at higher protospacer concentrations, potentially relevant to spacer acquisition from abundant pathogen RNAs or ssDNA fragments generated by phage defense nucleases. Our findings reveal mechanisms for site-specifically integrating RNA into DNA genomes with potential biotechnological applications.

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Evolutionary Classification of CRISPR‐Cas Systems

Cited by 15 publications

References 138 publications

CRISPR/Cas9 Systems and Gene Editing Technology

CRISPR/Cas9 Systems and Gene Editing Technology

New Insights for Biosensing: Lessons from Microbial Defense Systems

Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase–Cas1 fusion protein

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