Review
Microbiology
Florian Tesson, Aude Bernheim
Summary: Bacteria have a wide range of antiphage defense systems. Recent studies have found that these systems can be encoded within the same genome, suggesting possible interactions. This review explores the synergies and coregulations of these antiphage systems, suggesting a higher level of organization in prokaryotic antiviral defense similar to immune systems in animals and plants.
CURRENT OPINION IN MICROBIOLOGY
(2023)
Article
Cell Biology
Yilei Ma, Ru Zhao, Hui Guo, Qingchao Tong, Wallace Y. Langdon, Weiwei Liu, Jun Zhang, Jian Zhang
Summary: In this study, E-Syt1 was identified as a key regulator of Casp-11 oligomerization and activation. Macrophages lacking E-Syt1 showed reduced production of IL-1b and impaired pyroptosis. E-Syt1 underwent oligomerization and interacted with Casp-11 to facilitate its activation.
Article
Biochemistry & Molecular Biology
Rebecca K. Lau, Eray Enustun, Yajie Gu, Justin Nguyen, Kevin D. Corbett
Summary: Bacteria have evolved diverse immune systems to protect themselves from phage infection. Researchers have discovered a transcriptional regulator module associated with hundreds of CBASS immune systems and demonstrated its role in driving the expression of the CBASS system in response to DNA damage. This finding highlights a mechanism by which bacterial immune systems can sense and respond to cellular stress.
Article
Biology
Anastasiia Rusanova, Victor Fedorchuk, Stepan Toshchakov, Svetlana Dubiley, Dmitry Sutormin
Summary: This study provides insights into the metagenomics of three cold-water sponge species from the White Sea, revealing species-specific bacterial and viral communities associated with the sponges. The study also highlights the abundance of virus-host interactions within the sponge-associated community and the occurrence of viral exchanges between communities.
Article
Multidisciplinary Sciences
Ana Rita Narciso, Federico Iovino, Sigrun Thorsdottir, Peter Mellroth, Mario Codemo, Christian Spoerry, Francesco Righetti, Sandra Muschiol, Staffan Normark, Priyanka Nannapaneni, Birgitta Henriques-Normark
Summary: Intranasal immunization with pneumococcal membrane particles (MPs) provides excellent serotype-independent protection against invasive pneumococcal disease (IPD). The conserved lipoproteins MalX and PrsA are identified as the main antigens responsible for cross-protection. Omitting variable surface proteins and vaccine candidate PspA enhances protective immune responses to the conserved proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Sucharit Ray, Robyn Roth, Peter A. Keyel
Summary: Following membrane damage by bacterial cholesterol-dependent cytolysins, calcium influx activates mixed lineage kinase 3, which coordinates microvesicle shedding critical for cellular survival.
Article
Medicine, Research & Experimental
Ashot Sargsyan, Ludivine Doridot, Sarah A. Hannou, Wenxin Tong, Harini Srinivasan, Rachael Ivison, Ruby Monn, Henry H. Kou, Jonathan M. Haldeman, Michelle Arlotto, Phillip J. White, Paul A. Grimsrud, Inna Astapova, Linus T. Tsai, Mark A. Herman
Summary: A study found that carbohydrate response element-binding protein (ChREBP) regulates the activity of hepatocyte growth factor activator (HGFAC) in the liver, promoting glucose and lipid homeostasis and playing an important role in adapting to overnutrition.
Article
Virology
Anh Phuong Luu, Zhenlan Yao, Sangeetha Ramachandran, Stephanie A. Azzopardi, Linde A. Miles, William M. Schneider, H. -Heinrich Hoffmann, Leonia Bozzacco, Gustavo Garcia, Danyang Gong, Robert Damoiseaux, Hengli Tang, Kouki Morizono, Charles M. Rudin, Ren Sun, Vaithilingaraja Arumugaswami, John T. Poirier, Margaret R. MacDonald, Charles M. Rice, Melody M. H. Li
Summary: In the study, RhoV and WWTR1 were identified as important factors in early Zika virus infection, with RhoV playing a significant role in promoting viral infection and production. Additionally, RhoV was found to facilitate infection of certain flaviviruses and act at the viral entry step.
Article
Plant Sciences
Daisuke Mori, Ayane Moriyama, Hiroshi Kanamaru, Yoshinao Aoki, Yoshiyuki Masumura, Shunji Suzuki
Summary: The study demonstrates that electrical stimulation can induce plant defense response against fungal diseases through the SA-dependent defense pathway. This finding could help in developing a novel integrated pest management technique using electrical stimulation.
Article
Virology
Mitchell A. Pallett, Yongxu Lu, Geoffrey L. Smith
Summary: The transcription factors IRF3 and NF-kappa B play crucial roles in the immune response to viral and bacterial pathogens. This study identifies DDX50 as a factor that promotes the activation of the IRF3 signaling pathway in response to viral RNA or infection with RNA and DNA viruses. Deletion of DDX50 impairs IRF3 phosphorylation and the expression of genes and cytokines involved in the immune response. Loss of DDX50 also leads to increased replication and dissemination of various viruses. The findings highlight the important role of DDX50 as a broad-ranging viral restriction factor.
Article
Plant Sciences
Dongmei Zhang, Xingyi Shen, He Zhang, Xue Huang, Hanzi He, Junli Ye, Francesca Cardinale, Jihong Liu, Junwei Liu, Guohuai Li
Summary: This study reveals that the infection of Lasiodiplodia theobromae in peach trees leads to the accumulation of ethylene (ET) and jasmonic acid (JA), resulting in the production of gum. ET activates UDP-sugar metabolic genes and modulates JA and SA biosynthesis through the transcription factor EIL1, aggravating the development of gummosis.
HORTICULTURE RESEARCH
(2022)
Article
Biology
Pau Pascual-Garcia, Shawn C. Little, Maya Capelson
Summary: Cells are able to develop transcriptional memory after repeated exposure to external cues, and this memory can be maintained epigenetically through cell divisions with the help of a nuclear pore component called Nup98. This study used single-molecule RNA FISH to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. The results showed that cells rapidly activate a low-level transcriptional response upon hormone exposure, but also slowly transition into a specialized memory state characterized by a high rate of expression. It was found that this transition between non-memory and memory states is independent of the initial activation of transcription.
Article
Multidisciplinary Sciences
Giuseppe Federico Amodeo, Brenda Yasie Lee, Natalya Krilyuk, Carina Teresa Filice, Denis Valyuk, Daniel Erik Otzen, Sergey Noskov, Zoya Leonenko, Evgeny V. Pavlov
Summary: The c subunit is an inner mitochondrial membrane protein that plays a role in ATP synthase and stress-induced mitochondrial permeability changes. Research suggests that c subunit is amyloidogenic, forming oligomers and exhibiting ion channel activity in the presence of calcium ions. Toxic effects of c subunit may be linked to its amyloidogenic properties similar to neurodegenerative polypeptides.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Md Ashrafuzzaman
Summary: In this study, it was found that the co-presence of GS and CDs in model membranes significantly enhances the pore or defect formation potency of CDs, leading to considerable cytotoxicity in lipid bilayers.
Article
Virology
Dior Beerens, Sandra Franch-Arroyo, Timothy J. Sullivan, Christian Goosmann, Volker Brinkmann, Emmanuelle Charpentier
Summary: Bacteriophages impose strong evolutionary pressure on their microbial hosts, leading bacteria to develop sophisticated immune systems for protection. Streptococcus pyogenes prophages play a significant role in the pathogen's virulence, and the bacteria utilize mechanisms such as the CRISPR-Cas system and membrane vesicles to defend against phage predation.
Article
Biochemistry & Molecular Biology
Alexandra East-Seletsky, Mitchell R. O'Connell, David Burstein, Gavin J. Knott, Jennifer A. Doudna
Review
Biochemistry & Molecular Biology
Mitchell R. O'Connell
JOURNAL OF MOLECULAR BIOLOGY
(2019)
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
Multidisciplinary Sciences
Jung-Un Park, Amy Wei-Lun Tsai, Eshan Mehrotra, Michael T. Petassi, Shan-Chi Hsieh, Ailong Ke, Joseph E. Peters, Elizabeth H. Kellogg
Summary: CRISPR-associated transposition systems allow integration of a single DNA cargo directed by guide RNA in one orientation at a fixed distance from a programmable target sequence. Cryo-EM was used to characterize the transposition regulator TnsC, revealing the mechanism behind transposase polarity information transfer. Mechanistic findings include polymerization of ATP-bound TnsC helical filaments, TniQ capping the TnsC filament, and transposase-driven disassembly for element delivery only to unused protospacers. These findings provide a foundation for engineering CRISPR-associated transposition systems for research and therapeutic applications.
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
Jung-Un Park, Amy Wei-Lun Tsai, Tiffany H. Chen, Joseph E. Peters, Elizabeth H. Kellogg
Summary: This study reveals the conformation and mechanistic relationships of the transposase component TnsB in CRISPR-associated transposons, providing insights into its role in transposon integration. The structural information presented here will guide future work in modifying these systems as programmable gene integration tools.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Brandon Joseph Davis Burris, Adrian Moises Molina Vargas, Brandon J. Park, Mitchell R. O'Connell
Summary: This paper describes a method for Cas13-mediated RNA knockdown experiments, which involves thorough testing of the Cas13 ortholog to use, the duration of the experiment, the amount of transfected DNA, and methods for analyzing knockdown efficiency. The optimized protocol outlined in this paper provides a faster and more reliable approach for testing gRNA performance and target gene knockdown.
Article
Chemistry, Multidisciplinary
Jacob Waitkus, Yu Chang, Li Liu, Srinivasu Valagerahally Puttaswamy, Taerin Chung, Adrian M. Molina Vargas, Stephen J. Dollery, Mitchell R. O'Connell, Haogang Cai, Gregory J. Tobin, Nikhil Bhalla, Ke Du
Summary: A novel localized surface plasmon resonance (LSPR) system based on the coupling of gold nanomushrooms (AuNMs) and gold nanoparticles (AuNPs) has been developed to achieve a significant plasmonic resonant shift. By optimizing the size, surface chemistry, and concentration of the AuNPs, the LSPR effect can be maximized. This system has been integrated with a CRISPR-Cas13a RNA detection assay for the detection of SARS-CoV-2 RNA targets, providing a simple, specific, isothermal, and label-free molecular diagnostic system.
ADVANCED MATERIALS INTERFACES
(2023)
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)