Article
Microbiology
Gregory H. Babunovic, Michael A. DeJesus, Barbara Bosch, Michael R. Chase, Thibault Barbier, Amy K. Dickey, Bryan D. Bryson, Jeremy M. Rock, Sarah M. Fortune
Summary: The study found that the application of all-trans-retinoic acid (ATRA) can enhance the control of Mycobacterium tuberculosis (Mtb) by human macrophages, which is achieved by altering macrophage cholesterol trafficking and lipid metabolism. In addition, CRISPR interference screening was used to identify specific genes required for Mtb survival in ATRA-activated macrophages.
Article
Microbiology
Gregory H. Babunovic, Michael A. DeJesus, Barbara Bosch, Michael R. Chase, Thibault Barbier, Amy K. Dickey, Bryan D. Bryson, Jeremy M. Rock, Sarah M. Fortune
Summary: This study identifies that the treatment with ATRA can enhance the control ability of macrophages against Mycobacterium tuberculosis (Mtb) by affecting bacterial clearance through changes in macrophage cholesterol metabolism, and conducts the first Mtb CRISPR interference screen in the infection model, revealing certain Mtb genes specifically required to survive in ATRA-activated macrophages.
Article
Multidisciplinary Sciences
Olga Musharova, Sofia Medvedeva, Evgeny Klimuk, Noemi Marco Guzman, Daria Titova, Victor Zgoda, Anna Shiriaeva, Ekaterina Semenova, Konstantin Severinov, Ekaterina Savitskaya
Summary: This study describes a priming adaptation mode in the Type I CRISPR-Cas system, which enables specific and efficient spacer acquisition in cells. The research found that both Cas1 and Cas3 can directly bind to prespacers, implying a direct physical interaction between the interference and adaptation machineries.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Arvind Sharma, Michael N. Pham, Jeremiah B. Reyes, Randeep Chana, Won C. Yim, Chan C. Heu, Donghun Kim, Duverney Chaverra-Rodriguez, Jason L. Rasgon, Robert A. Harrell, Andrew B. Nuss, Monika Gulia-Nuss
Summary: Ticks have the ability to transmit various debilitating pathogens, but research on ticks has been lacking compared to other arthropod vectors due to challenges in applying genetic and molecular tools. This study reports a successful embryo injection protocol for the black-legged tick and demonstrates the use of CRISPR-Cas9 for genome editing. The results provide innovative tools for tick research.
Article
Biochemical Research Methods
Zhixia Ye, Eirik A. Moreb, Shuai Li, Juliana Lebeau, Romel Menacho-Melgar, Matthew Munson, Michael D. Lynch
Summary: CRISPR-based interference is widely used in various applications, with recent research focusing on the use of the native CRISPR Cascade system in E. coli for gene silencing. The instability of guide arrays used for dynamic silencing is attributed to the expression of the Cas1/2 endonuclease complex, leading to the loss of spacer sequences. A proposed model suggests that basal Cas1/2 endonuclease activity causes this loss, with mutant guide arrays being amplified through selection. Replacing a constitutive promoter with a tightly controlled inducible promoter improves guide array stability and minimizes leaky gene silencing, showing promise in avoiding CRISPR-based autoimmunity.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Cell Biology
Junyu Wu, Chunyan Wu, Fan Xing, Liu Cao, Weijie Zeng, Liping Guo, Ping Li, Yongheng Zhong, Hualian Jiang, Manhui Luo, Guang Shi, Lang Bu, Yanxi Ji, Panpan Hou, Hong Peng, Junjiu Huang, Chunmei Li, Deyin Guo
Summary: A novel nucleic acid-based antiviral system named ERASE has been discovered in mouse embryonic stem cells, which suppresses RNA virus infection by DNA-mediated RNA cleavage. The system involves reverse transcription of viral RNA into vcDNA by endogenous RTase, followed by the formation of DNA/RNA hybrids that are subsequently destroyed by cellular RNase H1, leading to suppression of viral growth.
Article
Multidisciplinary Sciences
Viktor Mamontov, Alexander Martynov, Natalia Morozova, Anton Bukatin, Dmitry B. Staroverov, Konstantin A. Lukyanov, Yaroslav Ispolatov, Ekaterina Semenova, Konstantin Severinov
Summary: This study demonstrates that plasmids can persist for multiple generations in certain Escherichia coli cell lineages under continuous targeting by the type I-E CRISPR-Cas system. The researchers propose that this complex dynamic process provides long-term benefits for bacterial populations by maintaining mobile genetic elements in some cells, leading to phenotypic diversification and rapid changes in the population structure to meet the demands of a changing environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Immunology
Christian Moebs, Martin Salheiser, Fabian Bleise, Marie Witt, Johannes U. Mayer
Summary: This review aims to highlight the role of basophils in antigen presentation and T cell priming, as well as resolving the debate on whether basophils influence antigen presentation through direct or indirect mechanisms. Tissue-specific differences in basophil phenotypes and their interactions with other antigen-presenting cells will be discussed, along with their implications on immunological and clinical outcomes of disease.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Ho Joung Lee, Hyun Ju Kim, Sang Jun Lee
Summary: In this study, we successfully constructed a CRISPR-Cas9 genome editing system to manipulate the genome of Enterobacterial phage A. By introducing mutations and expressing antisense mRNA, we were able to change the properties of the phage and demonstrate a method to control lysogenic cells.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Joseph M. Replogle, Jessica L. Bonnar, Angela N. Pogson, Christina R. Liem, Nolan K. Maier, Yufang Ding, Baylee J. Russell, Xingren Wang, Kun Leng, Alina Guna, Thomas M. Norman, Ryan A. Pak, Daniel M. Ramos, Michael E. Ward, Luke A. Gilbert, Martin Kampmann, Jonathan S. Weissman, Marco Jost
Summary: This study presents next-generation CRISPRi sgRNA libraries and effector expression constructs that enable strong and consistent knockdown of genes in mammalian cell models. These findings provide best practices for CRISPRi genetic screening.
Article
Biotechnology & Applied Microbiology
Camilo Calvache, Marta Vazquez-Vilar, Sara Selma, Mireia Uranga, Asun Fernandez-del-Carmen, Jose-Antonio Daros, Diego Orzaez
Summary: This study demonstrates that anti-CRISPR proteins AcrIIA4 and AcrVA1 can prevent CRISPR/Cas-mediated gene editing in plants, opening up new possibilities for customized control of gene editing and gene expression.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Infectious Diseases
Chen-Yi Cheung, Matthew B. McNeil, Gregory M. Cook
Summary: This study demonstrates the utility of CRISPRi in analyzing gene function and essentiality of Mycobacterium tuberculosis, and it can also be applied in intracellular M. tuberculosis infection models.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Manling Zhang, Ruchao Peng, Qi Peng, Sheng Liu, Zhiteng Li, Yuqin Zhang, Hao Song, Jia Yang, Xiao Xing, Peiyi Wang, Jianxun Qi, George F. Gao
Summary: CRISPR-Cas systems are commonly used in prokaryotes as adaptive antiviral systems. Phages can encode compact or incomplete CRISPR-Cas systems to suppress host defense mechanisms and establish infection. The phage ICP1 encodes a compact type I-F CRISPR-Cas system to inhibit antiphage genetic elements in its host, but the mechanism of target DNA recognition and interference remains unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Cara Adolph, Matthew B. McNeil, Gregory M. Cook
Summary: New drugs are urgently needed to combat tuberculosis. This study provides insight into the importance of succinate oxidation in Mycobacterium tuberculosis and the consequences of inhibiting this process. Additionally, the study shows that impaired succinate oxidation affects the activity of anti-tuberculosis drugs. These findings are valuable for the development of bioenergetic inhibitors.
Article
Biotechnology & Applied Microbiology
Jian Wang, Yuxi Teng, Xinyu Gong, Jianli Zhang, Yifei Wu, Lei Lou, Michelle Li, Zhong-Ru Xie, Yajun Yan
Summary: The RNA-guided Cas9 is a powerful tool for gene editing, but it is limited by the PAM sequence. This study identified three rare PAM-binding motifs among Streptococci Cas9 orthologs and investigated the specificity and recognition mechanism of one motif. By designing a minimal mutation, a new Cas9 variant with expanded PAM specificity was created, which significantly increased the production of a target compound in bacteria. This work provides new insights into Cas9 scaffolds and expands the possibilities of gene control.
METABOLIC ENGINEERING
(2023)