Article
Biochemistry & Molecular Biology
Maha Osman Hammad
Summary: This study modified the standard TRIzol RNA extraction method to establish a reproducible, applicable, and efficient protocol for extracting intact RNA from RNase-rich rat pancreas. The modified protocol yielded significantly higher RNA concentration and improved RNA purity compared to the standard protocol. RT-qPCR analysis also showed that the RNA extracted using the modified protocol had better quality, reflected by decreased Ct values.
PROCESS BIOCHEMISTRY
(2023)
Article
Genetics & Heredity
Tala Bakheet, Khalid S. A. Khabar, Edward G. Hitti
Summary: This study reveals that mRNAs containing AREs are preferentially upregulated in response to SARS-CoV-2 infection globally. Particularly, they are most highly upregulated in mild COVID-19 cases. The levels of these ARE-mRNAs, measured by RNA-seq, may serve as a reliable indication of COVID-19 severity.
Article
Biochemistry & Molecular Biology
Matthew C. Johnson, Eric Laderman, Erin Huiting, Chi Zhang, Alan Davidson, Joseph Bondy-Denomy
Summary: Bacteria have a wide range of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Hidden Markov Models were developed to analyze defense systems in microbial genomes and it was found that Pseudomonas aeruginosa has the highest diversity of anti-phage systems. Two core defense hotspots, cDHS1 and cDHS2, were identified and these regions are commonly found in P. aeruginosa isolates. The discovery of new anti-phage systems in these regions could simplify immune system research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Merel Derksen, Vicky Mertens, Eline A. Visser, Janine Arts, Wilma Vree Egberts, Ger J. M. Pruijn
Summary: RNase MRP is a ribonucleoprotein complex involved in endoribonucleolytic cleavage and is related to cartilage hair hypoplasia. By fusing a streptavidin-binding RNA aptamer, the S1m-aptamer, to the RNase MRP RNA, the relative expression levels of wildtype and mutant MRP RNAs can be compared, and active RNase MRP complexes can be isolated. Mutant MRP RNAs have lower expression levels and catalytic activity compared to the wildtype RNA, and a single nucleotide substitution at position 40 in the P3 domain reduces the binding of the Rpp25 protein subunit.
Article
Virology
Takeshi Kuroshima, Aya Yanagawa Matsuda, Elora Hossain, Motoaki Yasuda, Tetsuya Kitamura, Yoshimasa Kitagawa, Fumihiro Higashino
Summary: In adenovirus-infected cells, virus mRNAs are selectively transported into the cytoplasm by virus early gene products, facilitating virus replication. Ribonucleoprotein (RNP) granules in the cytoplasm, involved in mRNA degradation, were analyzed to understand the mechanism of ARE-mRNA stabilization in adenovirus-infected cells. It was found that processing bodies (PBs) aggregate and are then translocated to aggresomes formed by adenoviral gene products. E4orf3 was required for PBs translocation, and the same domains of E4orf3-mutants needed for changing the form of promyelocytic leukemia bodies were also necessary for PBs translocation. Luciferase activity assays showed that these domains were critical for miRNA- and ARE-mediated mRNA decay. These findings suggest that adenovirus alters the behavior of PBs to prevent downregulation of ARE-mRNA.
Article
Chemistry, Multidisciplinary
Jiuxing Li, Shadman Khan, Jimmy Gu, Carlos D. M. Filipe, Tohid F. Didar, Yingfu Li
Summary: An Au-on-Au tip sensor is developed for the detection of Salmonella using a new synthetic nucleic acid probe as a linker. The sensor can visually detect the presence of Salmonella by cleaving the probe and detecting the freed DNA-conjugated Au nanoparticle. It has a portable design without requiring any electronic, electrochemical or optical equipment, and shows a high detection limit and no cross-reactivity with control bacteria.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Markus Goessringer, Nadine B. Waeber, Jana C. Wiegard, Roland K. Hartmann
Summary: A small group of bacteria possess two types of RNase P, RNP RNase P and protein-only RNase P HARP. The dual RNase P activities of five bacteria from three phyla have been characterized. Among them, the thermophile Thermodesulfatator indicus has robust tRNA 5'-end maturation activity, suggesting both types of RNase P contribute to this activity. Additionally, T. indicus RNase P RNA undergoes posttranscriptional excision and fragmentation in vivo, which may be beneficial for RNA folding and enzymatic activity.
Article
Clinical Neurology
Xiao Chen, Ying Xu, Maode Wang, Chunying Ren
Summary: A risk model constructed by 10 differentially expressed AREs-related genes accurately predicts the prognosis of patients with GBM. Higher risk scores are associated with lower survival probability in GBM patients. The risk model has decent predictive power and the risk score and treatment type are independent prognostic indicators. The 10 biomarkers identified in this study may serve as important prognostic markers and potential therapeutic targets for GBM patients.
WORLD NEUROSURGERY
(2023)
Article
Microbiology
Daniel G. Mediati, David Lalaouna, Jai J. Tree
Summary: Regulatory RNAs play essential roles in gene regulation in bacteria, adopting diverse mechanisms in different species. Variations in RNA degradation and regulation mechanisms between bacterial species may lead to functional differences in Hfq and other sRNA chaperones.
Article
Plant Sciences
Chitose Honsho, Koichiro Ushijima, Misa Anraku, Shuji Ishimura, Qibin Yu, Frederick G. Gmitter, Takuya Tetsumura
Summary: This study identified genes regulating self-incompatibility in Japanese citrus cultivars through RNA-seq, revealing that six T2 RNase genes were S-RNases. The findings support the notion that citrus self-incompatibility is based on S-RNase. Further homology comparisons with S-RNases from Chinese citrus led to the conclusion that three of the T2 RNases were novel citrus S-RNases involved in self-incompatibility.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Nayef Jarrous, Dhivakar Mani, Aravind Ramanathan
Summary: The article discusses the coordination of transcription and processing of RNA in eukaryotes as a basic principle of gene expression regulation. It presents a model of high molecular weight initiation complexes of human RNA polymerase III on tRNA genes, highlighting their role in co-transcriptional processing of tRNA precursors to mature forms.
Review
Neurosciences
Ascension Ariza-Mateos, Carlos Briones, Celia Perales, Francisco Sobrino, Esteban Domingo, Jordi Gomez
Summary: Studies with RNA enzymes and protein enzymes have identified structural elements in cellular mRNAs and viral RNAs that have common structural folds and may have an ancient and common origin. The term 'mRNA archaeology' refers to the search for these ancient RNA elements, which can provide insights into early evolutionary developments. These RNA elements may have developed as biological signals with structural and functional relevance, coexisting with the linear information of nucleic acid molecules.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Biochemistry & Molecular Biology
Jamie Richards, Joel G. Belasco
Summary: Riboswitches are known to modulate transcription elongation or translation initiation, but a study on guanidine III riboswitch reveals that ligand binding can also protect mRNA from degradation by creating a structure that impedes scanning by regulatory endonuclease RNase E. This finding suggests that riboswitch aptamers can independently regulate gene expression by prolonging mRNA longevity in response to ligand binding.
Article
Biochemical Research Methods
Alicia Climent-Catala, Thomas E. Ouldridge, Guy-Bart Stan, Wooli Bae
Summary: Synthetic RNA systems have advantages over protein-based networks in terms of faster response, increased specificity, and programmability. In this study, we developed an in vitro RNA toggle switch using RNA aptamers to inhibit the transcriptional activity of two different RNA polymerases. The switch was successfully controlled by adding DNA sequences. The results demonstrated that the RNA-based toggle switch has potential applications in synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Neil R. Lloyd, Deborah S. Wuttke
Summary: Cyp33 is an essential human cyclophilin prolyl isomerase that plays various roles in splicing and chromatin remodeling, particularly through direct interaction with the MLL1 complex. Understanding how RNA binding drives the action of Cyp33 reveals its regulatory mechanism and interaction with the MLL1 complex.