Review
Microbiology
Sandra C. Garrett
Summary: CRISPR-Cas is a unique prokaryotic immune system that provides sequence-specific adaptive protection and can be updated in response to new threats. This system stores DNA fragments from invading genetic elements and continuously updates them, while regulating spacer uptake, residency, and loss for optimized immunity.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Yuping Li, Joseph Bondy-Denomy
Summary: Bacteriophages encode diverse anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas immunity during infection of their bacterial hosts. Instead of a single phage shutting down CRISPR-Cas immunity, a community of acr-carrying phages cooperate to suppress bacterial immunity, displaying low phage autonomy. Enzymatic Acr proteins with novel mechanisms have been recently revealed and are predicted to enhance phage autonomy, while phage DNA protective measures offer the highest phage autonomy observed. These varied Acr mechanisms and strengths also have unexpected impacts on the bacterial populations and competing phages.
CELL HOST & MICROBE
(2021)
Article
Microbiology
Kate Mortensen, Tony J. Lam, Yuzhen Ye
Summary: In this study, CRISPR-Cas systems in ESKAPE pathogens and Clostridium difficile were annotated and compared using publicly available genome sequences. The distribution of CRISPR-Cas systems in these pathogens showed a wide spectrum, with Staphylococcus aureus having the least tendency and C. difficile showing presence of multiple CRISPRs in each isolate. Statistical tests revealed that isolates containing CRISPR-Cas systems tend to have more antimicrobial resistance genes in A. baumannii, E. faecium, P. aeruginosa, and S. aureus. This annotated data is made available on a website for further research and potential clinical applications against antibiotic-resistant pathogens.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Ville Hoikkala, Janne Ravantti, Cesar Diez-Villasenor, Marja Tiirola, Rachel A. Conrad, Mark J. McBride, Sylvain Moineau, Lotta-Riina Sundberg
Summary: This study found that a specific CRISPR-Cas immune system, which is unable to acquire new spacers, can borrow acquisition machinery from another CRISPR-Cas locus to successfully acquire new spacers. These new spacers mainly target the viral genome, supporting the concept of collaboration between different CRISPR-Cas systems.
Article
Multidisciplinary Sciences
Daniel M. Sapozhnikov, Moshe Szyf
Summary: PROTECTOR is a novel approach that uses a nuclease-dead Cas protein to bind to off-target sites and interfere with Cas activity, reducing off-target mutation rates without compromising on-target activity. It can be used in combination with high-fidelity Cas enzymes to further decrease off-target editing, offering an ability to protect off-target sites with identical sequences to target sites.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Florian Stoertz, Peter Minary
Summary: With the advancement of CRISPR/Cas programmable nuclease system, in vivo therapeutic gene editing applications are becoming more feasible. However, concerns over non-negligible off-target effects remain prominent. crisprSQL is an interactive collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching cleavage profiling, gene editing safety analysis, and transcriptomics.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Pharmacology & Pharmacy
Duohao Ren, Sylvain Fisson, Deniz Dalkara, Divya Ail
Summary: Inherited retinal diseases are a major cause of blindness, and gene therapy using gene editing techniques like CRISPR-Cas9 shows promise for their treatment. However, ocular gene therapies can elicit immune responses that need to be managed to ensure safe and effective gene editing.
Article
Biochemistry & Molecular Biology
Shrutee Jakhanwal, Brady F. Cress, Pascal Maguin, Marco J. Lobba, Luciano A. Marraffini, Jennifer A. Doudna
Summary: CRISPR-Cas9 is an RNA-guided DNA endonuclease used in bacterial adaptive immunity and genome editing. This study reveals that the Cas9 supercomplex can generate trimmed DNA molecules required for genome integration, showing a distinct catalytic capacity for immunological memory in prokaryotes. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming independently of the guide RNA sequence.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Virology
Dmitriy Mazurov, Lama Ramadan, Natalia Kruglova
Summary: Rapid progress has been made in gene editing using CRISPR/Cas, but the clinical utility is limited due to delivery difficulties and potential off-target effects. Using CRISPR as a ribonucleoprotein (RNP) complex can reduce exposure time and off-target activity. Current delivery systems focus on packaging and delivering CRISPR/Cas RNPs using retro/lentiviral particles and exosomes. The mechanism of viral and exosomal particle formation, release, and entry helps to understand RNP packaging and uncoating. This review also discusses the passive loading of RNPs into exosomes and the mechanisms involved in particle fusion, RNP release, and transportation inside target cells, which can significantly influence the editing efficiency.
Review
Cell Biology
Yanping Hu, Wei Li
Summary: Abundant CRISPR-Cas systems provide valuable resources for developing versatile tools in biological discovery and disease treatment. This review discusses the development of CRISPR-Cas based tools and explores potential directions for future novel CRISPR toolkits.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Editorial Material
Plant Sciences
Andrea Giordano
Summary: CRISPR/Cas technology is a versatile genome editing system that is being used to address various challenges in agriculture. Tang et al. (2023) combined CRISPR/Cas9 with Agrobacterium virulence proteins and achieved a significant increase in genome editing frequency. This system was validated in rice and has the potential to be applied in genome engineering of agronomic traits and other species in the future.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Magdalena Hryhorowicz, Daniel Lipinski, Joanna Zeyland
Summary: The bacteria-derived CRISPR/Cas system is a versatile tool for genome engineering, with wide applications in various fields. However, challenges like immunological reactions and off-target effects remain. This review discusses the current classification of CRISPR systems, new genome-editing technologies, recent applications, as well as limitations, ethical issues, and challenges associated with the CRISPR/Cas system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Helen B. Belato, George P. Lisi
Summary: The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has revolutionized the field of CRISPR-Cas technology. These inhibitors have diverse structures and functions, and can act as orthosteric or allosteric inhibitors, as well as modify CRISPR-Cas components. Understanding the mechanisms of Acrs is crucial for the development of more precise and controllable CRISPR-Cas tools.
Article
Biochemistry & Molecular Biology
Rebecca E. McKenzie, Emma M. Keizer, Jochem N. A. Vink, Jasper van Lopik, Ferhat Bueke, Vera Kalkman, Christian Fleck, Sander J. Tans, Stan J. J. Brouns
Summary: The study reveals that CRISPR interference is fast and has a narrow distribution of clearance times. However, invaders with escaping mutations show large cell-to-cell variability, which stems from primed CRISPR adaptation. The growth rate, cell division, and Cascade levels of bacteria influence the chances of clearance by interference or priming.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Fisheries
Sumi Jung, Myoung-Jin Kim, Sarithaa Sellaththurai, Suna Kim, Seongdo Lee, Jehee Lee
Summary: The tetraspanin superfamily proteins are transmembrane proteins involved in various biological functions, including cell differentiation, adhesion, migration, signal transduction, intracellular trafficking, and immune responses. This study characterized the cd63 gene in a zebrafish model, showing its conservation in structural features and expression in immune system organs. By establishing cd63-deficient zebrafish lines using CRISPR/Cas9 system, the study provided a model for investigating the roles of cd63 in viral infection in vivo.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Florence Depardieu, David Bikard
Review
Microbiology
Antoine Vigouroux, David Bikard
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2020)
Article
Biochemistry & Molecular Biology
Alicia Calvo-Villamanan, Jerome Wong Ng, Remi Planel, Herve Menager, Arthur Chen, Lun Cui, David Bikard
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Aleksandra Nivina, Maj Svea Grieb, Celine Loot, David Bikard, Jean Cury, Laila Shehata, Juliana Bernardes, Didier Mazel
Review
Microbiology
Francois Rousset, David Bikard
CURRENT OPINION IN MICROBIOLOGY
(2020)
Article
Microbiology
Francois Rousset, Jose Cabezas-Caballero, Florence Piastra-Facon, Jesus Fernandez-Rodriguez, Olivier Clermont, Erick Denamur, Eduardo P. C. Rocha, David Bikard
Summary: Bacteria from the same species can vary widely in their gene content, leading to significant differences in gene essentiality between strains and conditions. Genetic determinants for these variations emphasize the importance of epistatic interactions with mobile genetic elements, particularly in triggering the essentiality of persistent genes.
NATURE MICROBIOLOGY
(2021)
Article
Biology
David Ranava, Yiying Yang, Luis Orenday-Tapia, Francois Rousset, Catherine Turlan, Violette Morales, Lun Cui, Cyril Moulin, Carine Froment, Gladys Munoz, Jerome Rech, Julien Marcoux, Anne Caumont-Sarcos, Cecile Albenne, David Bikard, Raffaele Ieva
Summary: Integral outer membrane proteins are crucial for maintaining envelope permeability in Proteobacteria, and DolP, a sigma(E)-upregulated outer membrane lipoprotein, is essential for fitness under envelope stress by interacting with the BAM complex and supporting OMP biogenesis. DolP's association with the mid-cell is linked to regulating septal peptidoglycan remodeling, and during envelope stress, this association is lost, potentially affecting cell division regulation.
Correction
Microbiology
Francois Rousset, Jose Cabezas-Caballero, Florence Piastra-Facon, Jesus Fernandez-Rodriguez, Olivier Clermont, Erick Denamur, Eduardo P. C. Rocha, David Bikard
NATURE MICROBIOLOGY
(2021)
Correction
Microbiology
Francois Rousset, Jose Cabezas-Caballero, Florence Piastra-Facon, Jesus Fernandez-Rodriguez, Olivier Clermont, Erick Denamur, Eduardo P. C. Rocha, David Bikard
Summary: The correction to this paper has been published.
NATURE MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Cyril Malbranke, David Bikard, Simona Cocco, Remi Monasson
Summary: This study introduces a new framework to assess the quality of generated protein sequences' secondary structures in comparison to reference structures for the family. Two scoring functions, Dot Product and Pattern Matching, are introduced and tested on experimental protein mutagenesis and design dataset, showing improvement in identifying nonfunctional sequences. The use of these scores also helps in rejecting nonfunctional sequences generated by graphical models learned from homologous sequence alignments.
Article
Mechanics
Matthew R. Walker, Marija Vucelja
Summary: The study considers the thermal relaxation of a particle in a piecewise-constant potential landscape and the connection between the Mpemba effect, metastable states, and phase transitions. The Mpemba effect is found to exist even in cases without metastable states and the borders of the areas where the effect happens correspond to either eigenvector changes of direction or to phase transitions. Discussions on the topological aspects of the strong Mpemba effect and proposing the use of topology to search for the Mpemba effect in a physical system are also presented.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Biochemistry & Molecular Biology
Eduardo P. C. Rocha, David Bikard
Summary: Prokaryotes possess mobile genetic elements that enable horizontal gene transfer between cells. These elements contain defense systems to filter, control, or inactivate other elements. The abundance of defense systems in these mobile genetic elements sheds new light on their role as tools of intragenomic conflict.
Article
Physics, Multidisciplinary
Hanqing Zhao, Marija Vucelja
Summary: We introduce an efficient nonreversible Markov chain Monte Carlo algorithm for generating self-avoiding walks with a variable endpoint, and compare its performance with existing algorithms in two and three dimensions.
FRONTIERS IN PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
William Rostain, Theophile Grebert, Danylo Vyhovskyi, Paula Thiel Pizarro, Gatwa Tshinsele-Van Bellingen, Lun Cui, David Bikard
Summary: Off-target binding of Cas9 to essential gene promoters can occur with as little as 4 nt of identity in the PAM-proximal sequence, leading to toxicity. This potential for off-target effects must be considered in CRISPR-Cas experiments in bacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Physics, Fluids & Plasmas
Depei Zhang, Tianran Chen, Marija Vucelja, Seung-Hun Lee, Gia-Wei Chern
Summary: This study introduces an efficient dynamical tree method to demonstrate the thermoremanent magnetization memory effect and condensation effect in a hierarchical energy landscape, showing the structural phase transition of the multilayer tree model coinciding with the onset of the condensation phenomenon. The results highlight the importance of hierarchical structure and the close relationship between glassy behavior and structure of barrier trees.