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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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Abstract
Microscopy is often used to assist the development of cheese products, but manufacturers can benefit from a much broader application of these techniques to assess structure formation during processing and structural changes during storage. Microscopy can be used to benchmark processes, optimize process variables, and identify critical control points for process control. Microscopy can also assist the reverse engineering of desired product properties and help troubleshoot production problems to improve cheese quality. This approach can be extended using quantitative analysis, which enables further comparisons between structural features and functional measures used within industry, such as cheese meltability, shreddability, and stretchability, potentially allowing prediction and control of these properties. This review covers advances in the analysis of cheese microstructure, including new techniques, and outlines how these can be applied to understand and improve cheese manufacture.
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Affiliation(s)
- Lydia Ong
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia; .,Dairy Innovation Hub, Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, Australia
| | - Xu Li
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia;
| | - Adabelle Ong
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia; .,Dairy Innovation Hub, Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, Australia
| | - Sally L Gras
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia; .,Dairy Innovation Hub, Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, Australia
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [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: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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Vink JNA, Brouns SJJ, Hohlbein J. Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis. Biophys J 2020; 119:1970-1983. [PMID: 33086040 DOI: 10.1016/j.bpj.2020.09.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/29/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022] Open
Abstract
Single-particle tracking is an important technique in the life sciences to understand the kinetics of biomolecules. The analysis of apparent diffusion coefficients in vivo, for example, enables researchers to determine whether biomolecules are moving alone, as part of a larger complex, or are bound to large cellular components such as the membrane or chromosomal DNA. A remaining challenge has been to retrieve quantitative kinetic models, especially for molecules that rapidly switch between different diffusional states. Here, we present analytical diffusion distribution analysis (anaDDA), a framework that allows for extracting transition rates from distributions of apparent diffusion coefficients calculated from short trajectories that feature less than 10 localizations per track. Under the assumption that the system is Markovian and diffusion is purely Brownian, we show that theoretically predicted distributions accurately match simulated distributions and that anaDDA outperforms existing methods to retrieve kinetics, especially in the fast regime of 0.1-10 transitions per imaging frame. AnaDDA does account for the effects of confinement and tracking window boundaries. Furthermore, we added the option to perform global fitting of data acquired at different frame times to allow complex models with multiple states to be fitted confidently. Previously, we have started to develop anaDDA to investigate the target search of CRISPR-Cas complexes. In this work, we have optimized the algorithms and reanalyzed experimental data of DNA polymerase I diffusing in live Escherichia coli. We found that long-lived DNA interaction by DNA polymerase are more abundant upon DNA damage, suggesting roles in DNA repair. We further revealed and quantified fast DNA probing interactions that last shorter than 10 ms. AnaDDA pushes the boundaries of the timescale of interactions that can be probed with single-particle tracking and is a mathematically rigorous framework that can be further expanded to extract detailed information about the behavior of biomolecules in living cells.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands; Microspectroscopy Reasearch Facility, Wageningen University & Research, Wageningen, the Netherlands.
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Wang Y, Fei J. Continuous active development of super-resolution fluorescence microscopy. Phys Biol 2020; 17:030401. [PMID: 32066124 DOI: 10.1088/1478-3975/ab7731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, AK 72701, United States of America. Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AK 72701, United States of America. Microelectronics-Photonics Program, University of Arkansas, Fayetteville, AK 72701, United States of America. Author to whom any correspondence should be addressed
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Martens KJA, van Beljouw SPB, van der Els S, Vink JNA, Baas S, Vogelaar GA, Brouns SJJ, van Baarlen P, Kleerebezem M, Hohlbein J. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nat Commun 2019; 10:3552. [PMID: 31391532 PMCID: PMC6685946 DOI: 10.1038/s41467-019-11514-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas9 is widely used in genomic editing, but the kinetics of target search and its relation to the cellular concentration of Cas9 have remained elusive. Effective target search requires constant screening of the protospacer adjacent motif (PAM) and a 30 ms upper limit for screening was recently found. To further quantify the rapid switching between DNA-bound and freely-diffusing states of dCas9, we developed an open-microscopy framework, the miCube, and introduce Monte-Carlo diffusion distribution analysis (MC-DDA). Our analysis reveals that dCas9 is screening PAMs 40% of the time in Gram-positive Lactoccous lactis, averaging 17 ± 4 ms per binding event. Using heterogeneous dCas9 expression, we determine the number of cellular target-containing plasmids and derive the copy number dependent Cas9 cleavage. Furthermore, we show that dCas9 is not irreversibly bound to target sites but can still interfere with plasmid replication. Taken together, our quantitative data facilitates further optimization of the CRISPR-Cas toolbox.
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Affiliation(s)
- Koen J A Martens
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Bionanotechnology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Sam P B van Beljouw
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Simon van der Els
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
- NIZO food research, Kernhemseweg 2, 6718 ZB, Ede, The Netherlands
| | - Jochem N A Vink
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Sander Baas
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - George A Vogelaar
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Microspectroscopy Research Facility, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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