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.
Article
Biochemistry & Molecular Biology
Beibei Wang, Tianlong Zhang, Jun Yin, You Yu, Wenhao Xu, Jianping Ding, Dinshaw J. Patel, Hui Yang
Summary: Bacteria and archaea use CRISPR-Cas surveillance complexes to defend against foreign invaders by capturing and integrating invading genetic elements into the CRISPR array for sequence-specific DNA/RNA targeting and cleavage. Recent studies have shown that target RNAs with specific complementarity can reduce Cas13a system's RNA cleavage, providing insights for regulating Cas13a cleavage activity.
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)
Article
Biology
Lucy Chou-Zheng, Asma Hatoum-Aslan
Summary: The CRISPR-Cas system is an adaptive immune system that protects prokaryotes from invading plasmids and viruses. This study identifies RNase R as a critical nuclease in completing crRNA maturation and its specific interactions with the type III effector complex member Csm5. The study also demonstrates the importance of RNase R and PNPase in maintaining robust anti-plasmid immunity.
Review
Medicine, General & Internal
Shiu-Jau Chen, Chung- Rai, Shao-Cheng Wang, Yuan-Chuan Chen
Summary: The early detection of infectious diseases and microorganisms is crucial for effective disease treatment, control, and prevention. Currently, nucleic acid testing and antigen-antibody serum reaction are widely used methods, but they have limitations. Therefore, the development of a quick and on-site diagnostic test based on CRISPR/Cas technology is necessary.
Review
Pathology
V. Edwin Hillary, Savarimuthu Ignacimuthu, S. Antony Ceasar
Summary: Multiple research groups are exploring the potential of CRISPR-based tools for rapid detection of COVID-19, with expectations for novel kits for mass detection in the future, indicating optimism that science will ultimately triumph over the pandemic.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2021)
Review
Biochemistry & Molecular Biology
Pilar Puig-Serra, Maria Cruz Casado-Rosas, Marta Martinez-Lage, Beatriz Olalla-Sastre, Alejandro Alonso-Yanez, Raul Torres-Ruiz, Sandra Rodriguez-Perales
Summary: CRISPR/Cas is a prokaryotic self-defense system widely used as a gene-editing tool, while also being adapted for nucleic acid detection. The rapid expansion of CRISPR diagnostics in the past 5 years has led to FDA-authorized COVID-19 tests and the establishment of multiple companies. CRISPR-based detection methods offer high sensitivity, reproducibility, versatility, and multiplexing capability, while also being cost-effective and requiring minimal laboratory settings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Richard Bauer, Dorina Haider, Aline Grempels, Rebecca Roscher, Stefanie Mauerer, Barbara Spellerberg
Summary: This study analyzed the CRISPR-Cas systems in Streptococcus anginosus and found two types of CRISPR-Cas II systems. One type contained a long csn2 gene, similar to Streptococcus thermophilus, while the other type contained a short csn2 gene, similar to S. pyogenes.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Xiaoping Li, Jiaye Zhong, Haoyu Li, Yinbiao Qiao, Xiaolei Mao, Huayan Fan, Yiwu Zhong, Saber Imani, Shusen Zheng, Jianhui Li
Summary: CRISPR-Cas technology is a widely used gene editing tool in biology, microbiology, and other fields. It consists of highly conserved repetitive sequences and spacer sequences, and utilizes the endonuclease activity of Cas proteins, combined with signal amplification and transformation technologies, to rapidly detect pathogen nucleic acids.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Peipei Yin, Yi Zhang, Lingguang Yang, Yue Feng
Summary: Bacteria and archaea have developed the CRISPR-Cas system as an adaptive defense mechanism against mobile genetic elements, but these elements have also evolved anti-CRISPR proteins to counteract the immune defenses. This review focuses on the non-canonical inhibition strategies adopted by these proteins and provides insights into the ongoing arms race between prokaryotic hosts and their predators.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Microbiology
Elvis Quansah, Yihuan Chen, Shijie Yang, Junyan Wang, Danhong Sun, Yangxi Zhao, Ming Chen, Li Yu, Chao Zhang
Summary: Genomic editing is essential for understanding the biology of Plasmodium and developing diagnostic tools and therapeutic targets. Recent advances in genomic diagnostic technologies and genetic manipulation tools have allowed editing at the DNA, RNA, and protein level. The CRISPR-Cas13 system, which can specifically bind and cut RNA, shows promise in Plasmodium research with its advantages and limitations.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ahmed Mahas, Tin Marsic, Mauricio Lopez-Portillo Masson, Qiaochu Wang, Rashid Aman, Cheng Zheng, Zahir Ali, Madain Alsanea, Ahmed Al-Qahtani, Bernard Ghanem, Fatimah Alhamlan, Magdy Mahfouz
Summary: This study identified and characterized a thermally stable ortholog of the Cas13a family, TccCas13a, and developed a sensitive and rapid assay called OPTIMA-dx for the detection of SARS-CoV-2 using TccCas13a. The assay demonstrated high specificity and sensitivity, and was suitable for multiplexed detection. The findings highlight the potential of CRISPR-Cas13 thermostable enzymes in POC diagnostics and other applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Matvey V. Kolesnik, Iana Fedorova, Karyna A. Karneyeva, Daria N. Artamonova, Konstantin V. Severinov
Summary: The Type III CRISPR-Cas system, despite being among the most common, is one of the least investigated gene defense systems due to its complexity. This system recognizes and destroys foreign nucleic acids, with its effector complexes specifically targeting and cleaving RNA molecules.
BIOCHEMISTRY-MOSCOW
(2021)
Review
Biotechnology & Applied Microbiology
Xiaolei Mao, Minghui Xu, Shuyin Luo, Yi Yang, Jiaye Zhong, Jiawei Zhou, Huayan Fan, Xiaoping Li, Zhi Chen
Summary: In the field of pathogen detection, isothermal amplification technology is an important alternative to traditional PCR due to its speed, accuracy, and sensitivity. This paper explores the principles and current status of recombinase polymerase amplification (RPA) and recombinase-aid amplification (RAA), as well as the integration of the CRISPR-Cas system with these techniques. Furthermore, the paper reviews the combination of isothermal amplification and CRISPR-Cas technology and its practical applications in pathogen detection, highlighting the significant advancements it brings to research and clinical implementation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
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)
Article
Biochemistry & Molecular Biology
Enbo Ma, Lucas B. Harrington, Mitchell R. O'Connell, Kaihong Zhou, Jennifer A. Doudna
Article
Biochemistry & Molecular Biology
David A. Nelles, Mark Y. Fang, Mitchell R. O'Connell, Jia L. Xu, Sebastian J. Markmiller, Jennifer A. Doudna, Gene W. Yeo
Article
Multidisciplinary Sciences
Alexandra East-Seletsky, Mitchell R. O'Connell, Spencer C. Knight, David Burstein, Jamie H. D. Cate, Robert Tjian, Jennifer A. Doudna
Article
Biochemistry & Molecular Biology
Alexandra East-Seletsky, Mitchell R. O'Connell, David Burstein, Gavin J. Knott, Jennifer A. Doudna
Article
Biochemistry & Molecular Biology
Gavin J. Knott, Alexandra East-Seletsky, Joshua C. Cofsky, James M. Holton, Emeric Charles, Mitchell R. O'Connell, Jennifer A. Doudna
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Gavin J. Knott, Alexandra East-Seletsky, Joshua C. Cofsky, James M. Holton, Emeric Charles, Mitchell R. O'Connell, Jennifer A. Doudna
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Mitchell R. O'Connell, Benjamin L. Oakes, Samuel H. Sternberg, Alexandra East-Seletsky, Matias Kaplan, Jennifer A. Doudna
Article
Multidisciplinary Sciences
Molly K. Clifton, Belinda J. Westman, Sock Yue Thong, Mitchell R. O'Connell, Michael W. Webster, Nicholas E. Shepherd, Kate G. Quinlan, Merlin Crossley, Gerd A. Blobel, Joel P. Mackay
Article
Cell Biology
Akshay Tambe, Alexandra East-Seletsky, Gavin J. Knott, Jennifer A. Doudna, Mitchell R. O'Connell
Editorial Material
Biochemistry & Molecular Biology
Brandon J. Davis, Mitchell R. O'Connell
Article
Biochemistry & Molecular Biology
Ethan J. Walker, John Q. Bettinger, Kevin A. Welle, Jennifer R. Hryhorenko, Adrian M. Molina Vargas, Mitchell R. O'Connell, Sina Ghaemmaghami
Summary: This study provides proteome-wide evidence that the thermodynamic folding stability of proteins strongly influences the oxidation rates of buried methionine residues. These findings highlight the utility of using oxidation rates as a metric of folding stability and suggest a correlation between folding stability and optimal growth temperatures.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Arica R. VanderWal, Jung-Un Park, Bogdan Polevoda, Julia K. Nicosia, Adrian M. Molina Vargas, Elizabeth H. Kellogg, Mitchell R. O'Connell
Summary: In this study, researchers discovered that the membrane protein Csx28 in Type VI CRISPR-Cas systems enhances antiviral defense by slowing cellular metabolism upon viral infection. The antiviral activity of Csx28 requires sequence-specific cleavage of viral messenger RNAs by Cas13b. High-resolution cryo-electron microscopy revealed that Csx28 forms an octameric pore-like structure, which localizes to the inner membrane in vivo.
Article
Biochemistry & Molecular Biology
Souvik Sinha, Adrian M. Molina Vargas, Pablo R. Arantes, Amun Patel, Mitchell R. O'Connell, Giulia Palermo
Summary: Cas13a is a recent addition to the CRISPR-Cas toolkit that specifically targets RNA for detection purposes. This study reveals that target RNA acts as an allosteric effector, amplifying communication signals to control RNA cleavage activity. The findings provide a fundamental understanding of the mechanism of action of Cas13a and open up new avenues for the development of highly selective RNA-based cleavage and detection tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Adrian M. Molina Vargas, Souvik Sinha, Raven Osborn, Pablo R. Arantes, Amun Patel, Stephen Dewhurst, Dwight J. Hardy, Andrew Cameron, Giulia Palermo, Mitchell R. O'Connell
Summary: The increasing demand for sensitive, fast, and inexpensive nucleic acid-based detection technologies in clinical diagnostics has led to the successful application of RNA-guided ribonuclease CRISPR-Cas13. However, detecting genetic variations, such as single-nucleotide polymorphisms, remains challenging. In this study, the researchers expanded their understanding of LbuCas13a RNA detection specificity and developed novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. These advancements allowed for superior discrimination of SARS-CoV-2 strains compared to the wild-type LbuCas13a. These findings provide new design criteria and Cas13a variants for future Cas13-based RNA detection applications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)