Article
Biochemistry & Molecular Biology
Zhongxia Yi, Rene M. Arvola, Sean Myers, Corinne N. Dilsavor, Rabab Abu Alhasan, Bayley N. Carter, Robert D. Patton, Ralf Bundschuh, Guramrit Singh
Summary: This study reveals that nonsense-mediated mRNA decay (NMD) in human cell lines can be dependent on UPF3B or independent of it. UPF3A only weakly activates NMD in wild-type cells, but strongly activates NMD in cells lacking UPF3B.
Article
Multidisciplinary Sciences
Oh Sung Kwon, Rahul Mishra, Adham Safieddine, Emeline Coleno, Quentin Alasseur, Marion Faucourt, Isabelle Barbosa, Edouard Bertrand, Nathalie Spassky, Herve Le Hir
Summary: Exon junction complexes (EJCs) mark untranslated spliced mRNAs and play a crucial role in mRNA lifecycle. This study demonstrates the accumulation of EJCs at basal bodies of mNSC or RPE1 cells, affecting cell differentiation and growth. The down-regulation of EJCs impairs centriolar material organization and ciliogenesis, suggesting that EJC-dependent mRNA trafficking towards centrosomes and basal bodies is important for proper mNSC division and brain development.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jun Katahira, Tatsuya Ohmae, Mayo Yasugi, Ryosuke Sasaki, Yumi Itoh, Tomoko Kohda, Miki Hieda, Masami Yokota Hirai, Toru Okamoto, Yoichi Miyamoto
Summary: To facilitate replication, viruses can block host gene expression by targeting processes such as mRNA nuclear export. In this study, it was found that Nsp14, a viral replicase subunit, inhibits mRNA nuclear export, leading to accumulation of RNA in the cell nucleus and disruption of nuclear speckles. Dysregulation of splicing and mRNA processing was observed in SARS-CoV-2-infected cells. The inhibitory activities of Nsp14 were diminished by a mutation in its guanine-N7-methyltransferase active site. The compromise of the nuclear cap-binding complex (NCBC) function by N7-methyl-GTP, produced in Nsp14-expressing cells, leads to defects in mRNA processing and export, representing a novel viral strategy to block host gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Immunology
Andrei A. Deviatkin, Ruslan A. Simonov, Kseniya A. Trutneva, Anna A. Maznina, Anastasiia B. Soroka, Anna A. Kogan, Sofya G. Feoktistova, Elena M. Khavina, Olga N. Mityaeva, Pavel Y. Volchkov
Summary: Recently, the mRNA platform has become the method of choice in vaccine development to find new ways to fight infectious diseases. However, mRNA vaccines have the drawback of requiring special storage conditions, making them less accessible. Circular mRNAs have been proposed as a solution to this problem, as they lack the ends that are susceptible to degradation. This review summarizes the current knowledge on cap-independent translation initiation methods for circular mRNAs and discusses their potential effectiveness in developing vaccines and other biotechnological products.
Article
Biochemistry & Molecular Biology
William R. Brothers, Farah Ali, Sam Kajjo, Marc R. Fabian
Summary: The interaction between XRN1 and EDC4 regulates P-body dynamics to properly coordinate mRNA decapping with 5'-3' decay in human cells. Disrupting this interaction or altering their stoichiometry inhibits mRNA decapping and leads to larger P-bodies. P-bodies support cell viability and prevent stress granule formation when XRN1 is limiting.
Review
Cell Biology
Christelle Morris, David Cluet, Emiliano P. Ricci
Summary: Eukaryotic gene expression is regulated by the translation and turnover of mRNAs, with the ribosome playing a central role in this process. The cell has evolved multiple translation-dependent mRNA surveillance pathways to handle specific problematic mRNAs. Current research focuses on translation features, genetic code complexity, and the emerging role of the ribosome as a regulatory hub.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Biochemistry & Molecular Biology
Martyna Nowacka, Przemyslaw Latoch, Matylda A. Izert, Natalia K. Karolak, Rafal Tomecki, Michal Koper, Agnieszka Tudek, Agata L. Starosta, Maria W. Gorna
Summary: This study proposes an mRNA enrichment strategy based on the RNA-binding properties of human IFIT1, which effectively depletes rRNA while maintaining high quality RNA-seq data with coverage of the protein coding transcriptome. It is a cost-effective and versatile tool for preparing mRNA libraries for various organisms.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jake C. Swartzel, Michael J. Bond, Andreas P. Pintado-Urbanc, Mehana Daftary, Mackenzie W. Krone, Todd Douglas, Evan J. Carder, Joshua T. Zimmer, Takahiro Maeda, Matthew D. Simon, Craig M. Crews
Summary: The RNA decapping scavenger protein DcpS has been identified as a dependency in acute myeloid leukemia (AML), and its inhibition or knockdown shows antiproliferative effects on AML cells. The non-essential nature of DcpS in normal human hematopoietic cells suggests potential for therapeutic intervention in AML by modulating DcpS activity. JCS-1, a PROTAC developed in this study, effectively degrades DcpS in nanomolar concentrations, offering a new strategy for AML and other DcpS-dependent genetic disorders.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Vinay K. Nagarajan, Catherine J. Stuart, Anna T. DiBattista, Monica Accerbi, Jeffrey L. Caplan, Pamela J. Green
Summary: In plants, cytoplasmic mRNA decay controlled by DNE1 is crucial for gene expression and RNA homeostasis. Using RNA degradome approaches, this study identified over 200 DNE1 substrates, primarily cleaved within coding regions. While most DNE1 targets were NMD-insensitive, some were NMD-sensitive, indicating its role in turnover of diverse mRNAs. Mutations in the endoribonuclease domain of DNE1 abolished the cleavage, demonstrating its requirement for activity. This work provides important insights into DNE1-mediated mRNA decay.
Review
Biochemistry & Molecular Biology
Qiushuang Wu, Ariel A. Bazzini
Summary: Messenger RNA (mRNA) stability and translational efficiency play crucial roles in protein production. Recent studies have shown that ribosomes, in addition to protein synthesis, also control mRNA stability in a codon-dependent manner known as codon optimality. Codons have a significant impact on mRNA stability and provide cis-regulatory information beyond their encoding amino acids. The molecular mechanism of codon optimality is still not fully understood, but it appears that the translation elongation rate triggers mRNA decay, where transfer RNAs may serve as master gene regulators influencing mRNA stability. This article discusses the findings of codon optimality and gene regulation related to codon composition in different eukaryotic species.
ANNUAL REVIEW OF BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jagadeesh Kumar Uppala, Leena Sathe, Abhijit Chakraborty, Sankhajit Bhattacharjee, Anthony Thomas Pulvino, Madhusudan Dey
Summary: Translation of HAC1 mRNA in budding yeast is regulated by nonconventional splicing and interactions between the 5'-UTR and intron. At least 11-base-pairing interactions between the 5'-UTR and intron are sufficient to repress HAC1 translation, and overexpression of the helicase eukaryotic initiation factor 4A can derepress translation of unspliced HAC1 mRNA with 11-bp interactions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Jesus Fernandez-Abascal, Lei Wang, Bianca Graziano, Christina K. Johnson, Laura Bianchi
Summary: Transcriptional adaptation is a gene regulation mechanism that increases genetic stability. This study reveals the occurrence of transcriptional adaptation in the C. elegans clh family of Cl- channels, which requires the involvement of exon-junction complex (EJC) proteins. Different clh genes are regulated by the EJC in different ways.
Article
Biochemistry & Molecular Biology
Cheuk Hei Ho, Chiara Paolantoni, Praveen Bawankar, Zuojian Tang, Stuart Brown, Jean-Yves Roignant, Jessica E. Treisman
Summary: The exon junction complex regulates various functions related to mRNA splicing, translation, degradation, and localization, with Barentsz playing a distinct role in Drosophila neuromuscular development. Barentsz is involved in mitochondrial distribution and synapse growth, independent of its interactions with the exon junction complex. Additionally, Barentsz influences synapse growth through the regulation of Activin ligand Dawdle expression.
Article
Cell Biology
Kiril Tishinov, Anne Spang
Summary: Translation repressor Scd6 and decapping stimulator Edc3 partially redundantly regulate P-body assembly by sequestering the Dcp1/2 decapping complex in the cytoplasm. Nuclear Dcp1/2 is not involved in mRNA decay and might be stored as a releasable pool, indicating a dynamic equilibrium between cytoplasmic and nuclear Dcp1/2.
JOURNAL OF CELL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Chen Liu, Andriani Mentzelopoulou, Ioannis H. Hatzianestis, Epameinondas Tzagkarakis, Vasileios Skaltsogiannis, Xuemin Ma, Vassiliki A. Michalopoulou, Francisco J. Romero-Campero, Ana B. Romero-Losada, Panagiotis F. Sarris, Peter Marhavy, Bettina Boelter, Alexandros Kanterakis, Emilio Gutierrez-Beltran, Panagiotis N. Moschou
Summary: This study presents a proximity-biotinylation approach for capturing the RNAs in cellular condensates known as processing bodies (PBs). The researchers found that the RNA composition in PBs is more dynamic compared to the total transcriptome. They identified enriched RNAs involved in cell wall development, plant hormonal signaling, and RNA metabolism within PBs. The study also revealed that RNA-binding proteins and the liquidity of PBs modulate RNA recruitment, and RNAs in PBs can have different fates depending on the size and type of the PB.
Article
Biochemical Research Methods
Rei-Lin Kuo, Zong-Hua Li, Li-Hsin Li, Kuo-Ming Lee, Ee-Hong Tam, Helene M. Liu, Hao-Ping Liu, Shin-Ru Shih, Chih-Ching Wu
JOURNAL OF PROTEOME RESEARCH
(2016)
Article
Microbiology
Chuan-Tien Hung, Yu-An Kung, Mei-Ling Li, Gary Brewer, Kuo-Ming Lee, Shih-Tung Liu, Shin-Ru Shih
Review
Biochemistry & Molecular Biology
Kuo-Ming Lee, Chi-Jene Chen, Shin-Ru Shih
TRENDS IN MICROBIOLOGY
(2017)
Article
Immunology
Kuo-Ming Lee, Yu-Nong Gong, Tzu-Hsuan Hsieh, Andrew Woodman, Nynke H. Dekker, Craig E. Cameron, Shin-Ru Shih
EMERGING MICROBES & INFECTIONS
(2018)
Article
Biochemistry & Molecular Biology
Kuo-Ming Lee, Woan-Yuh Tarn
NUCLEIC ACIDS RESEARCH
(2014)
Article
Virology
Andrew Woodman, Kuo-Ming Lee, Richard Janissen, Yu-Nong Gong, Nynke H. Dekker, Shin-Ru Shih, Craig E. Cameron
JOURNAL OF VIROLOGY
(2019)
Article
Biochemical Research Methods
Kuo-Ming Lee, Yu-Nong Gong, Shin-Ru Shih
Article
Biochemistry & Molecular Biology
Kuo-Ming Lee, Chih-Ching Wu, Shang-En Wu, Ya-Han Lin, Li-Ting Wang, Chun-Ru Chang, Peng-Nien Huang, Shin-Ru Shih, Rei-Lin Kuo
Article
Microbiology
Chung-Guei Huang, Kuo-Ming Lee, Mei-Jen Hsiao, Shu-Li Yang, Peng-Nien Huang, Yu-Nong Gong, Tzu-Hsuan Hsieh, Po-Wei Huang, Ya-Jhu Lin, Yi-Chun Liu, Kuo-Chien Tsao, Shin-Ru Shih
JOURNAL OF CLINICAL MICROBIOLOGY
(2020)
Article
Microbiology
Sheng-Yu Huang, Yu-An Kung, Peng-Nien Huang, Sheng-Yun Chang, Yu-Nong Gong, Yi-Ju Han, Huan-Jung Chiang, Kuan-Ting Liu, Kuo-Ming Lee, Chia-Yu Chang, Chia-Ching Chang, Chung-Guei Huang, Shin-Ru Shih
Summary: The study reveals that SARS-CoV-2 remains stable and infectious after refrigeration or freezing, with stability and infectivity depending on the spike variant. The S-G614 variant shows higher stability and better binding ability with the ACE2 receptor, contributing to its rapid spread and infectivity. Further precautions should be taken when handling food stored in cold conditions.
Review
Microbiology
Yu-An Kung, Kuo-Ming Lee, Huan-Jung Chiang, Sheng-Yu Huang, Chung-Jung Wu, Shin-Ru Shih
Summary: This review discusses the molecular mechanisms of SARS-CoV-2 and related coronaviruses, with a focus on host factors or pathways identified through genome-wide CRISPR screening that can be targeted for the development of effective antiviral agents.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Immunology
Guan-Hong Wu, Kuo-Ming Lee, Chia-Yu Kao, Shin-Ru Shih
Summary: The role of the internal ribosome entry site (IRES) in determining the neurovirulence of enteroviruses EV-A71 and CV-A16 was characterized using an oral inoculation model. Replacing EV-A71 IRES with CV-A16 abolished neuropathological phenotypes, indicating that IRES determines the neurotropic potential of these viruses. Tissue-specific replication can be reflected in cell-based characterization.
MICROBES AND INFECTION
(2023)
Article
Multidisciplinary Sciences
Tzu-Wei Chuang, Chia-Chen Lu, Chun-Hao Su, Pei-Yu Wu, Sarasvathi Easwvaran, Chi-Chieh Lee, Hung-Che Kuo, Kuan-Yang Hung, Kuo-Ming Lee, Ching-Yen Tsai, Woan-Yuh Tarn
Review
Biochemistry & Molecular Biology
Tzu-Wei Chuang, Kou-Ming Lee, Woan-Yuh Tarn