Article
Microbiology
Hannah N. Taylor, Eric Laderman, Matt Armbrust, Thomson Hallmark, Dylan Keiser, Joseph Bondy-Denomy, Ryan N. Jackson
Summary: This article summarizes recent advancements in understanding the function of type IV CRISPR systems. Through bioinformatic and structural analysis, insights are provided for future studies aiming to elucidate the function of these cryptic systems.
FRONTIERS IN MICROBIOLOGY
(2021)
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
Biology
Asgar H. Ansari, Manoj Kumar, Sajal Sarkar, Souvik Maiti, Debojyoti Chakraborty, Tony Yuen
Summary: CRISPR-based diagnostics (CRISPRDx) have improved clinical decision-making during the COVID-19 pandemic. A web server called CriSNPr is introduced for designing guide RNAs (gRNAs) and validating oligonucleotide sequences for CRISPRDx. CriSNPr also provides a database of pre-designed gRNAs and target/off-target information for human and SARS-CoV-2 variants. The versatility and applicability of CriSNPr have been validated on multiple Cas proteins.
Article
Biochemical Research Methods
Mario Escobar, Jing Li, Aditi Patel, Shizhe Liu, Qi Xu, Isaac B. Hilton
Summary: CRISPR/Cas technologies have revolutionized genome design and gene expression regulation. However, the efficacy of different CRISPR/Cas systems in human cells remains unclear, making it challenging to select the optimal technology and limiting its practical applications. In this study, a series of testbed systems were designed to evaluate the capabilities of 10 different Cas protein variants in genome editing, CRISPRi, and CRISPRa. The results show that Cas9 >= Cas12a > Cas12e/Cas12j are more effective in genome editing and CRISPRa applications.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Evan Brenner, Srinand Sreevatsan
Summary: The study found that mycobacterial CRISPR/Cas systems are widespread, with some species containing multiple types. Cas III-A systems were identified in pathogenic Mycobacterium heckeshornense and a geological environmental isolate Mycobacterium SM1. The findings suggest that CRISPR/Cas systems are unreliable markers for MTBC evolution, and horizontal gene transfer plays a frequent role in mycobacterial genetic variation.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Chemistry, Analytical
Chao Zhu, Fan Zhang, Huidong Li, Zilei Chen, Mengmeng Yan, Linsen Li, Feng Qu
Summary: This review comprehensively summarizes the recent progress of CRISPR/Cas system-based aptasensors (Cas-aptasensors) including their design principles and superior applications. It introduces the essential features of aptamers and the CRISPR/Cas system, outlines the composition of Cas-aptasensors, and emphasizes their fabrication methods, bio-recognition mechanism, and detection evaluation. It also discusses the challenges and future directions for aptamers, CRISPR/Cas systems, and their accelerating applications in Cas-aptasensors.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Microbiology
Coralie Lemaire, Brice Le Gallou, Philippe Lanotte, Laurent Mereghetti, Adeline Pastuszka
Summary: This review focuses on the distribution, diversity, and roles of CRISPR-Cas systems in main pathogenic streptococci. CRISPR-Cas systems act as adaptive immune systems and have applications in genome editing and analyzing bacterial interactions with the environment and evolution.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Vanja Perculija, Jinying Lin, Bo Zhang, Songying Ouyang
Summary: CRISPR-Cas systems are a form of prokaryotic adaptive immunity that use RNA-guided endonucleases to cleave foreign genetic elements, with great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors have been widely used in genome editing, the recent discovery of RNA-targeting CRISPR-Cas systems has shown promise for RNA manipulation as well.
Review
Chemistry, Physical
Xianlong Zhang, Yiheng Shi, Guang Chen, Di Wu, Yongning Wu, Guoliang Li
Summary: Rapid, sensitive, and accurate detection of pathogens is crucial for preventing infectious diseases and improving healthcare systems. Inspired by the CRISPR/Cas system, new biosensors have been developed and applied in the detection of infectious viruses and pathogenic bacteria.
Review
Microbiology
Marta Zakrzewska, Michal Burmistrz
Summary: The CRISPR-Cas system is a prokaryotic system that allows for specific recognition and cleavage of nucleic acids. It consists of a CRISPR array containing short DNA fragments called spacers that are complementary to the targeted nucleic acid, and Cas proteins that are involved in various processes. The primary role of the CRISPR-Cas system is to provide adaptive and hereditary immunity against exogenous nucleic acids. It has revolutionized gene editing and gene expression regulation in molecular biology.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Cong-Fei Xu, Guo-Jun Chen, Ying-Li Luo, Yue Zhang, Gui Zhao, Zi-Dong Lu, Anna Czarna, Zhen Gu, Jun Wang
Summary: The CRISPR-Cas system has revolutionized genome editing, but efficient delivery to target tissues/cells remains a challenge. This review summarizes the characteristics of different CRISPR-Cas therapeutic tools and investigates current in vivo delivery systems, emphasizing the requirements for efficient delivery in clinical settings and the safety of different tools.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Basem Al-Shayeb, Petr Skopintsev, Katarzyna M. Soczek, Elizabeth C. Stahl, Zheng Li, Evan Groover, Dylan Smock, Amy R. Eggers, Patrick Pausch, Brady F. Cress, Carolyn J. Huang, Brian Staskawicz, David F. Savage, Steven E. Jacobsen, Jillian F. Banfield, Jennifer A. Doudna
Summary: CRISPR-Cas systems are found not only in microbes, but also in bacteriophages. These systems have diverse anti-viral functions and new Cas9-like proteins have been discovered. Cas lambda, in particular, is capable of inducing genome editing in different types of cells.
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)
Article
Agronomy
Yong Huang, Huirong Dong, Meiqi Shang, Kejian Wang
Summary: With the increasing human population and deteriorating environment, there is a need to breed environmentally friendly and resource-conserving rice cultivars for sustainable agricultural development and food security. CRISPR/Cas technology allows efficient genome modification, promising higher yield, improved quality, and resistance in rice plants.
Review
Biotechnology & Applied Microbiology
Hai-Yan Yu, Shu-Guang Wang, Peng-Fei Xia
Summary: Global warming is becoming a serious problem due to human activities, particularly the emission of carbon dioxide. To address this challenge, reducing reliance on fossil fuels and capturing CO2 from the atmosphere are crucial. Carbon-neutral and carbon-negative biotechnologies, specifically those based on CO2-metabolizing microorganisms, have shown promise in producing fuels and chemicals. CRISPR-Cas systems have been developed to engineer these microorganisms and advance carbon-negative biotechnology. This review focuses on recent advances in applying CRISPR-Cas systems for genome editing and interference/activation in specific microorganisms and discusses potential future innovations.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Editorial Material
Microbiology
Rodolphe Barrangou, Luciano A. Marraffini
Summary: This article discusses the ability of CRISPR-Cas systems to integrate invasive DNA sequences and establish adaptive immunity in bacteria. The study by Dimitriu et al. demonstrates that bacteriostatic antibiotics can induce CRISPR acquisition events, highlighting the impact of environmental conditions on the complex dynamics between host and virus, as well as the corresponding biological and genetic arms race.
CELL HOST & MICROBE
(2022)
Article
Microbiology
Benjamin E. Rubin, Spencer Diamond, Brady F. Cress, Alexander Crits-Christoph, Yue Clare Lou, Adair L. Borges, Haridha Shivram, Christine He, Michael Xu, Zeyi Zhou, Sara J. Smith, Rachel Rovinsky, Dylan C. J. Smock, Kimberly Tang, Trenton K. Owens, Netravathi Krishnappa, Rohan Sachdeva, Rodolphe Barrangou, Adam M. Deutschbauer, Jillian F. Banfield, Jennifer A. Doudna
Summary: This study presents a generalizable strategy for editing the genomes of specific organisms in microbial communities, using environmental transformation sequencing (ET-seq) and DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems to achieve species- and site-specific genetic manipulation.
NATURE MICROBIOLOGY
(2022)
Editorial Material
Genetics & Heredity
Rodolphe Barrangou
Article
Microbiology
MaryClaire Chamberlain, Sarah O'Flaherty, Natalia Cobian, Rodolphe Barrangou
Summary: Lactobacillus species are important residents of the human gastrointestinal tract that can be influenced by probiotic supplements and dietary changes, ultimately affecting host health. The growth of four Lactobacillus strains in the presence of pomegranate extract was studied, revealing the production of unique metabolites. Untargeted metabolomics was utilized to further characterize the metabolic profiles of these strains. Understanding these differences is crucial for understanding probiotic function and selecting strains for commercial products.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Meichen Pan, Wesley Morovic, Claudio Hidalgo-Cantabrana, Avery Roberts, Kimberly K. O. Walden, Yong Jun Goh, Rodolphe Barrangou
Summary: This study repurposed the endogenous type I-G CRISPR-Cas system and an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, showcasing the impact of genomic and epigenetic contexts on editing outcomes across strains. Additionally, a CRISPR-cytosine base editor was optimized to sensitize multiple B. lactis strains to tetracycline by introducing C.G-to-T.A mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Daniel F. M. Monte, Matthew A. Nethery, Hanna Berman, Shivaramu Keelara, Nilton Lincopan, Paula J. Fedorka-Cray, Rodolphe Barrangou, Mariza Landgraf
Summary: This study characterized the resistome, phylogenetic structure, and CRISPR array composition of Salmonella enterica serovar Heidelberg strains isolated from the poultry production chain in Brazil. The results showed that these strains have a broad host range and are multidrug-resistant, with a widespread distribution of antibiotic-resistant strains from farm to market. The study also highlights the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork and emphasizes the importance of CRISPR-based genotyping for salmonellae.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Benjamin A. Adler, Tomas Hessler, Brady F. Cress, Arushi Lahiri, Vivek K. Mutalik, Rodolphe Barrangou, Jillian Banfield, Jennifer A. Doudna
Summary: In this study, the defensive capabilities of LbuCas13a protein were analyzed, and it was found to have robust antiviral activity against a wide range of phages. By leveraging LbuCas13a targeting, successful genome editing of multiple phages was achieved, demonstrating the versatility and potency of Cas13a as a generalizable tool for editing diverse biological entities.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Sarah O'Flaherty, Natalia Cobian, Rodolphe Barrangou
Summary: This study examined the interaction between probiotic strains and a pomegranate extract, revealing that the extract had species-specific effects on the growth, cell survival, transcription, and metabolite formation of the bacteria. The findings support the growing interest in using pomegranate as a prebiotic compound.
Article
Microbiology
Matthew H. Foley, Morgan E. Walker, Allison K. Stewart, Sarah O'Flaherty, Emily C. Gentry, Shakshi Patel, Violet V. Beaty, Garrison Allen, Meichen Pan, Joshua B. Simpson, Caroline Perkins, Molly E. Vanhoy, Michael K. Dougherty, Sarah K. McGill, Ajay S. Gulati, Pieter C. Dorrestein, Erin S. Baker, Matthew R. Redinbo, Rodolphe Barrangou, Casey M. Theriot
Summary: Bile acids play a role in the interaction between human and microbial cells and affect diseases, including Clostridioides difficile infection (CDI). Bile salt hydrolases (BSHs) shape the bile acid pool by deconjugating conjugated BAs, but their selectivity and impact on C. difficile remain unclear. This study investigates the diversity of BSHs in gut commensals and other members of the human gut microbiome. The results show that BSHs with different specificities can restrict C. difficile growth in vitro and colonization in vivo models. Furthermore, BSHs can reshape the pool of microbial conjugated bile acids (MCBAs) in the gut and restrict C. difficile virulence in vitro.
NATURE MICROBIOLOGY
(2023)
Article
Food Science & Technology
Clinton A. Page, Ilenys M. Perez-Diaz, Meichen Pan, Rodolphe Barrangou
Summary: The study conducted a comparative genomic analysis on different Lactiplantibacillus strains in cucumber fermentation and identified distinct features between L. pentosus and L. plantarum. The study also revealed the diversity of L. pentosus in the fermentation habitat. These findings are important for the selection of functional starter cultures.
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Marena Trinidad, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M. Karp, Petr Skopintsev, Brittney W. Thornton, Rachel F. Weissman, Peter H. Yoon, Linxing Chen, Tomas Hessler, Amy R. Eggers, David Colognori, Ron Boger, Erin E. Doherty, Connor A. Tsuchida, Ryan Tran, Laura Hofman, Honglue Shi, Kevin M. Wasko, Zehan Zhou, Chenglong Xia, Muntathar J. Al-Shimary, Jaymin R. Patel, Vienna C. J. X. Thomas, Rithu Pattali, Matthew J. Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F. Maxwell, Andrew G. Murdock, Glenn C. Ramit, Hope R. Henderson, Roland W. Calvert, Rebecca S. Bamert, Gavin J. Knott, Audrone Lapinaite, Patrick Pausch, Joshua C. Cofsky, Erik J. Sontheimer, Blake Wiedenheft, Peter C. Fineran, Stan J. J. Brouns, Dipali G. Sashital, Brian C. Thomas, Christopher T. Brown, Daniela S. A. Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F. Banfield, David F. Savage, Jennifer A. Doudna
Summary: CRISPR-Cas enzymes play a crucial role in bacterial immunity and genome editing. CasPEDIA is a comprehensive database that summarizes the enzymatic properties of Cas enzymes, providing valuable resources for researchers.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daniel B. Sulis, Xiao Jiang, Chenmin Yang, Barbara M. Marques, Megan L. Matthews, Zachary Miller, Kai Lan, Carlos Cofre-Vega, Baoguang Liu, Runkun Sun, Henry Sederoff, Ryan G. Bing, Xiaoyan Sun, Cranos M. Williams, Hasan Jameel, Richard Phillips, Hou-min Chang, Ilona Peszlen, Yung-Yun Huang, Wei Li, Robert M. Kelly, Ronald R. Sederoff, Vincent L. Chiang, Rodolphe Barrangou, Jack P. Wang
Summary: This study demonstrates that multiplex CRISPR editing allows precise engineering of woody feedstock for improved lignin composition and wood properties, leading to more efficient fiber pulping and potential environmental benefits.
Article
Engineering, Biomedical
Ourania Raftopoulou, Rodolphe Barrangou
Summary: The discovery of novel CRISPR-Cas systems and their associated genome editing effectors is facilitated by the need for new genome manipulation tools. Researchers have analyzed prokaryotic genomes and metagenomic sequencing data to find diverse CRISPR-Cas systems. This review summarizes the in silico, in vitro, and in vivo analyses conducted to characterize key elements of CRISPR-Cas systems and validates their function in genome editing.
CURRENT OPINION IN BIOMEDICAL ENGINEERING
(2023)
Article
Genetics & Heredity
Brook Pyhtila, Seth Kasowitz, Rachel Leeson, Rodolphe Barrangou
Summary: CRISPR-based technologies have been rapidly distributed to academic institutions, enabling the democratization of genome editing. The requests for CRISPR plasmids continue to rise, reflecting the robust demand for various types of CRISPR effectors. Furthermore, there is a diversification of genome editing applications, with requests for mammalian, plant, and microbial constructs.
Meeting Abstract
Biotechnology & Applied Microbiology
Gabriel Butterfield, Dahlia Rohm, Avery Roberts, Matthew Nethery, Anthony Rizzo, Rodolphe Barrangou, Charles Gersbach