1
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Strohkendl I, Saha A, Moy C, Nguyen AH, Ahsan M, Russell R, Palermo G, Taylor DW. Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Mol Cell 2024:S1097-2765(24)00485-4. [PMID: 38955179 DOI: 10.1016/j.molcel.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables target recognition and nuclease activation, we used cryo-electron microscopy to capture wild-type Acidaminococcussp. Cas12a R-loop intermediates and DNA delivery into the RuvC active site. Stages of Cas12a R-loop formation-starting from a 5-bp seed-are marked by distinct REC domain arrangements. Dramatic domain flexibility limits contacts until nearly complete R-loop formation, when the non-target strand is pulled across the RuvC nuclease and coordinated domain docking promotes efficient cleavage. Next, substantial domain movements enable target strand repositioning into the RuvC active site. Between cleavage events, the RuvC lid conformationally resets to occlude the active site, requiring re-activation. These snapshots build a structural model depicting Cas12a DNA targeting that rationalizes observed specificity and highlights mechanistic comparisons to other class 2 effectors.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Aakash Saha
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Catherine Moy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alexander-Hoi Nguyen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
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2
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Olivi L, Bagchus C, Pool V, Bekkering E, Speckner K, Offerhaus H, Wu W, Depken M, Martens KA, Staals RJ, Hohlbein J. Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a. Nucleic Acids Res 2024; 52:5241-5256. [PMID: 38647045 PMCID: PMC11109954 DOI: 10.1093/nar/gkae283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Cleo Bagchus
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Victor Pool
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ezra Bekkering
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Konstantin Speckner
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hidde Offerhaus
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Wen Y Wu
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands
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3
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Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nat Commun 2024; 15:1473. [PMID: 38368461 PMCID: PMC10874386 DOI: 10.1038/s41467-024-45762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in which initial cleavage of the non-target strand is followed by target strand cleavage. How the spatially distant DNA target strand traverses toward the RuvC catalytic core is presently not understood. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal that an α-helical lid, located within the RuvC domain, plays a pivotal role in the traversal of the DNA target strand by anchoring the crRNA:target strand duplex and guiding the target strand toward the RuvC core, as also corroborated by DNA cleavage experiments. In this mechanism, the REC2 domain pushes the crRNA:target strand duplex toward the core of the enzyme, while the Nuc domain aids the bending and accommodation of the target strand within the RuvC core by bending inward. Understanding of this critical process underlying Cas12a activity will enrich fundamental knowledge and facilitate further engineering strategies for genome editing.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
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4
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Kim CH, Lee WJ, Oh Y, Lee Y, Lee HK, Seong JB, Lim KS, Park SJ, Huh JW, Kim YH, Kim KM, Hur JK, Lee SH. Utilization of nicking properties of CRISPR-Cas12a effector for genome editing. Sci Rep 2024; 14:3352. [PMID: 38336977 PMCID: PMC10858195 DOI: 10.1038/s41598-024-53648-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
The CRISPR-Cas nickase system for genome editing has attracted considerable attention owing to its safety, efficiency, and versatility. Although alternative effectors to Cas9 have the potential to expand the scope of genome editing, their application has not been optimized. Herein, we used an enhanced CRISPR-Cas12a nickase system to induce mutations by targeting genes in a human-derived cell line. The optimized CRISPR-Cas12a nickase system effectively introduced mutations into target genes under a specific directionality and distance between nickases. In particular, the single-mode Cas12a nickase system can induce the target-specific mutations with less DNA double-strand breaks. By inducing mutations in the Thymine-rich target genes in single- or dual-mode, Cas12a nickase compensates the limitations of Cas9 nickase and is expected to contribute to the development of future genome editing technologies.
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Grants
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- (22A0203L1) the Korean Fund for Regenerative Medicine (KFRM) grant funded by the Korea government (the Ministry of Science and ICT, the Ministry of Health & Welfare).
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Affiliation(s)
- Chan Hyoung Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Wi-Jae Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyomin K Lee
- Department of Medicine, Major in Medical Genetics, Graduate School, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jung Bae Seong
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Kyung-Seob Lim
- Futuristic Animal Resource and Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Sang Je Park
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Kyoung Mi Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea.
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea.
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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5
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Tenjo-Castaño F, Montoya G, Carabias A. Transposons and CRISPR: Rewiring Gene Editing. Biochemistry 2023; 62:3521-3532. [PMID: 36130724 PMCID: PMC10734217 DOI: 10.1021/acs.biochem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/11/2022] [Indexed: 11/30/2022]
Abstract
CRISPR-Cas is driving a gene editing revolution because of its simple reprogramming. However, off-target effects and dependence on the double-strand break repair pathways impose important limitations. Because homology-directed repair acts primarily in actively dividing cells, many of the current gene correction/replacement approaches are restricted to a minority of cell types. Furthermore, current approaches display low efficiency upon insertion of large DNA cargos (e.g., sequences containing multiple gene circuits with tunable functionalities). Recent research has revealed new links between CRISPR-Cas systems and transposons providing new scaffolds that might overcome some of these limitations. Here, we comment on two new transposon-associated RNA-guided mechanisms considering their potential as new gene editing solutions. Initially, we focus on a group of small RNA-guided endonucleases of the IS200/IS605 family of transposons, which likely evolved into class 2 CRISPR effector nucleases (Cas9s and Cas12s). We explore the diversity of these nucleases (named OMEGA, obligate mobile element-guided activity) and analyze their similarities with class 2 gene editors. OMEGA nucleases can perform gene editing in human cells and constitute promising candidates for the design of new compact RNA-guided platforms. Then, we address the co-option of the RNA-guided activity of different CRISPR effector nucleases by a specialized group of Tn7-like transposons to target transposon integration. We describe the various mechanisms used by these RNA-guided transposons for target site selection and integration. Finally, we assess the potential of these new systems to circumvent some of the current gene editing challenges.
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Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Arturo Carabias
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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6
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Rajasooriya T, Ogasawara H, Dong Y, Mancuso JN, Salaita K. Force-Triggered Self-Destructive Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305544. [PMID: 37724392 PMCID: PMC10764057 DOI: 10.1002/adma.202305544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Self-destructive polymers (SDPs) are defined as a class of smart polymers that autonomously degrade upon experiencing an external trigger, such as a chemical cue or optical excitation. Because SDPs release the materials trapped inside the network upon degradation, they have potential applications in drug delivery and analytical sensing. However, no known SDPs that respond to external mechanical forces have been reported, as it is fundamentally challenging to create mechano-sensitivity in general and especially so for force levels below those required for classical force-induced bond scission. To address this challenge, the development of force-triggered SDPs composed of DNA crosslinked hydrogels doped with nucleases is described here. Externally applied piconewton forces selectively expose enzymatic cleavage sites within the DNA crosslinks, resulting in rapid polymer self-degradation. The synthesis and the chemical and mechanical characterization of DNA crosslinked hydrogels, as well as the kinetics of force-triggered hydrolysis, are described. As a proof-of-concept, force-triggered and time-dependent rheological changes in the polymer as well as encapsulated nanoparticle release are demonstrated. Finally, that the kinetics of self-destruction are shown to be tuned as a function of nuclease concentration, incubation time, and thermodynamic stability of DNA crosslinkers.
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Affiliation(s)
| | | | - Yixiao Dong
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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7
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Tessmer I. The roles of non-productive complexes of DNA repair proteins with DNA lesions. DNA Repair (Amst) 2023; 129:103542. [PMID: 37453245 DOI: 10.1016/j.dnarep.2023.103542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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8
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Hussen BM, Rasul MF, Abdullah SR, Hidayat HJ, Faraj GSH, Ali FA, Salihi A, Baniahmad A, Ghafouri-Fard S, Rahman M, Glassy MC, Branicki W, Taheri M. Targeting miRNA by CRISPR/Cas in cancer: advantages and challenges. Mil Med Res 2023; 10:32. [PMID: 37460924 PMCID: PMC10351202 DOI: 10.1186/s40779-023-00468-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPR) has changed biomedical research and provided entirely new models to analyze every aspect of biomedical sciences during the last decade. In the study of cancer, the CRISPR/CRISPR-associated protein (Cas) system opens new avenues into issues that were once unknown in our knowledge of the noncoding genome, tumor heterogeneity, and precision medicines. CRISPR/Cas-based gene-editing technology now allows for the precise and permanent targeting of mutations and provides an opportunity to target small non-coding RNAs such as microRNAs (miRNAs). However, the development of effective and safe cancer gene editing therapy is highly dependent on proper design to be innocuous to normal cells and prevent introducing other abnormalities. This study aims to highlight the cutting-edge approaches in cancer-gene editing therapy based on the CRISPR/Cas technology to target miRNAs in cancer therapy. Furthermore, we highlight the potential challenges in CRISPR/Cas-mediated miRNA gene editing and offer advanced strategies to overcome them.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Kurdistan Region 44001 Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region 44001 Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region 44001 Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, Lebanese French University, Erbil, Kurdistan Region 44001 Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Kurdistan Region 44001 Iraq
| | - Goran Sedeeq Hama Faraj
- Department of Medical Laboratory Science, Komar University of Science and Technology, Sulaymaniyah, 46001 Iraq
| | - Fattma Abodi Ali
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region 44001 Iraq
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region 44001 Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, 44001 Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 374-37515 Iran
| | - Milladur Rahman
- Department of Clinical Sciences, Malmö, Section for Surgery, Lund University, 22100 Malmö, Sweden
| | - Mark C. Glassy
- Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, San Diego, CA 94720 USA
| | - Wojciech Branicki
- Faculty of Biology, Institute of Zoology and Biomedical Research, Jagiellonian University, 31-007 Kraków, Poland
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, 374-37515 Iran
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9
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Xu J, Liu Z, Zhang Z, Wu T. Unlocking the Full Potential of Cas12a: Exploring the Effects of Substrate and Reaction Conditions on Trans-Cleavage Activity. Anal Chem 2023. [PMID: 37392174 DOI: 10.1021/acs.analchem.3c01307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
The trans-cleavage activity of Cas12a has been widely used with various applications. Here, we report that the trans-cleavage activity of Cas12a can be significantly affected by the fluorescent probe length and reaction buffer. The optimal probe length for Cas12a is found to be 15 nucleotides, and the optimal buffer is NEBuffer 4. Compared to the popularly used reaction conditions, the activity of Cas12a is improved by about 50-fold. In addition, the detection limit of Cas12a for DNA targets has been reduced by nearly three orders of magnitude. Our method provides a powerful tool for Cas12a trans-cleavage activity applications.
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Affiliation(s)
- Jie Xu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhujun Liu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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10
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Gaillochet C, Peña Fernández A, Goossens V, D’Halluin K, Drozdzecki A, Shafie M, Van Duyse J, Van Isterdael G, Gonzalez C, Vermeersch M, De Saeger J, Develtere W, Audenaert D, De Vleesschauwer D, Meulewaeter F, Jacobs TB. Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform. Genome Biol 2023; 24:6. [PMID: 36639800 PMCID: PMC9838060 DOI: 10.1186/s13059-022-02836-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Testing an ever-increasing number of CRISPR components is challenging when developing new genome engineering tools. Plant biotechnology has few high-throughput options to perform iterative design-build-test-learn cycles of gene-editing reagents. To bridge this gap, we develop ITER (Iterative Testing of Editing Reagents) based on 96-well arrayed protoplast transfections and high-content imaging. RESULTS We validate ITER in wheat and maize protoplasts using Cas9 cytosine and adenine base editors (ABEs), allowing one optimization cycle - from design to results - within 3 weeks. Given that previous LbCas12a-ABEs have low or no activity in plants, we use ITER to develop an optimized LbCas12a-ABE. We show that sequential improvement of five components - NLS, crRNA, LbCas12a, adenine deaminase, and linker - leads to a remarkable increase in activity from almost undetectable levels to 40% on an extrachromosomal GFP reporter. We confirm the activity of LbCas12a-ABE at endogenous targets in protoplasts and obtain base-edited plants in up to 55% of stable wheat transformants and the edits are transmitted to T1 progeny. We leverage these improvements to develop a highly mutagenic LbCas12a nuclease and a LbCas12a-CBE demonstrating that the optimizations can be broadly applied to the Cas12a toolbox. CONCLUSION Our data show that ITER is a sensitive, versatile, and high-throughput platform that can be harnessed to accelerate the development of genome editing technologies in plants. We use ITER to create an efficient Cas12a-ABE by iteratively testing a large panel of vector components. ITER will likely be useful to create and optimize genome editing reagents in a wide range of plant species.
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Affiliation(s)
- Christophe Gaillochet
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Alexandra Peña Fernández
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Vera Goossens
- grid.11486.3a0000000104788040Screening Core, VIB, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.5342.00000 0001 2069 7798Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Katelijn D’Halluin
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
| | - Andrzej Drozdzecki
- grid.11486.3a0000000104788040Screening Core, VIB, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.5342.00000 0001 2069 7798Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Myriam Shafie
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
| | - Julie Van Duyse
- grid.11486.3a0000000104788040VIB Flow Core, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Gert Van Isterdael
- grid.11486.3a0000000104788040VIB Flow Core, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Camila Gonzalez
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jonas De Saeger
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Ward Develtere
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Dominique Audenaert
- grid.11486.3a0000000104788040Screening Core, VIB, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.5342.00000 0001 2069 7798Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - David De Vleesschauwer
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
| | - Frank Meulewaeter
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
| | - Thomas B. Jacobs
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
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Wang JY, Pausch P, Doudna JA. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Nat Rev Microbiol 2022; 20:641-656. [PMID: 35562427 DOI: 10.1038/s41579-022-00739-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, we examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications. We explore the adaptive and interference aspects of CRISPR-Cas function as well as open questions about the molecular mechanisms responsible for genome targeting. These structural insights reflect close evolutionary links between CRISPR-Cas systems and mobile genetic elements, including the origins and evolution of CRISPR-Cas systems from DNA transposons, retrotransposons and toxin-antitoxin modules. We discuss how the evolution and structural diversity of CRISPR-Cas systems explain their functional complexity and utility as genome editing tools.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Pausch
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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12
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Vasilev R, Gunitseva N, Shebanova R, Korzhenkov A, Vlaskina A, Evteeva M, Polushkina I, Nikitchina N, Toshchakov S, Kamenski P, Patrushev M, Mazunin I. Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii. Int J Mol Sci 2022; 23:ijms23169289. [PMID: 36012553 PMCID: PMC9409102 DOI: 10.3390/ijms23169289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from Ruminococcus bromii sp. entitled RbCas12a, which is able to efficiently cleave target DNA templates, using the particularly high accessibility of PAM 5′-YYN and a relatively wide temperature range from 20 °C to 42 °C. In comparison to Acidaminococcus sp. (AsCas12a) nuclease, RbCas12a is capable of processing DNA more efficiently, and can be active upon being charged by spacer-only RNA at lower concentrations in vitro. We show that the human-optimized RbCas12a nuclease is also active in mammalian cells, and can be applied for efficient deletion incorporation into the human genome. Given the advantageous properties of RbCas12a, this enzyme shows potential for clinical and biotechnological applications within the field of genome editing.
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Affiliation(s)
- Ruslan Vasilev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
| | - Natalia Gunitseva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Regina Shebanova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksei Korzhenkov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Anna Vlaskina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Marta Evteeva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Irina Polushkina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Natalia Nikitchina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- UMR7156–Molecular Genetics, Genomics, Microbiology, University of Strasbourg and Centre National de la Recherche Scientifique (CNRS), 67000 Strasbourg, France
| | - Stepan Toshchakov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maxim Patrushev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Ilya Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Medical Genomics LLC, 119192 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
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