Article
Multidisciplinary Sciences
Edward J. Sanderlin, Melissa M. Keenan, Martin Mense, Alexey S. Revenko, Brett P. Monia, Shuling Guo, Lulu Huang
Summary: This study reveals that CFTR mRNAs with nonsense codons are predominantly degraded by the SMG6-mediated branch of the NMD pathway. This finding provides potential strategies for the treatment of cystic fibrosis.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
James M. Burke, Nina Ripin, Max B. Ferretti, Laura A. St Clair, Emma R. Worden-Sapper, Fernando Salgado, Sara L. Sawyer, Rushika Perera, Kristen W. Lynch, Roy Parker
Summary: RNase L-mediated mRNA decay occurs primarily in the cytoplasm and leads to the re-localization of RNA-binding proteins from the cytoplasm to the nucleus. This re-localization coincides with altered RNA processing in the nucleus, particularly affecting mRNAs encoding interferons. Similar RNA processing defects are observed during dengue virus and SARS-CoV-2 infection. These findings uncover novel mechanisms by which RNase L regulates host gene expression and blocks protein synthesis.
Article
Microbiology
Jonas Henrique Costa, Jaqueline Moraes Bazioli, Luidy Darllan Barbosa, Pedro Luis Theodoro dos Santos Junior, Flavia C. G. Reis, Tabata Klimeck, Camila Manoel Crnkovic, Roberto G. S. Berlinck, Alessandra Sussulini, Marcio L. Rodrigues, Taicia Pacheco Fill
Summary: The study revealed a novel phytopathogenic role of P. digitatum EVs and tryptoquialanine A in causing damage to citrus fruits during infection, implying that this alkaloid is exported in EVs during plant infection.
Article
Biochemistry & Molecular Biology
Garima Dixit, Willow Schanz, Benjamin A. Pappas, Thorsten Maretzky
Summary: Metalloproteases ADAM10 and ADAM17 have been identified as differentially regulated FGFR membrane sheddases, playing roles in modulating FGFR signaling during cell migration. Ectodomain shedding can impact the function of ligand-induced FGFR signaling in cell movement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Environmental Sciences
Christoph Ruecker, Elisa Grabitz, Klaus Kuemmerer
Summary: Methylsiloxanes, compounds containing H3C-Si-O subunits, are pervasive environmental pollutants created through industrial production and widely used. Whether and to what extent microorganisms can degrade these compounds remains uncertain. This review critically examines existing evidence for and against microbial degradation of methylsiloxanes, particularly the cleavage of Si-CH3 bonds, finding no convincing proof of cleavage by native environmental microorganisms.
Article
Biology
Shunsuke Saito, Kazutoshi Mori
Summary: This protocol describes a method for detecting and quantifying calcium ions in the endoplasmic reticulum (ER) and cytoplasm of cultured cells using fluorescent reporter proteins and ImageJ software. The fluorescence brightness of cells expressing these reporter proteins reflects the calcium ion concentration in each intracellular region.
Article
Neurosciences
Yuqin Men, Haruki Higashimori, Kathryn Reynolds, Leona Tu, Rachel Jarvis, Yongjie Yang
Summary: This study investigates the role of FMRP in astroglial processes and reveals that the loss of FMRP affects mRNA localization and expression. These findings provide new insights into the interactions and signaling mechanisms between astroglial processes and synapses.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mahmoud Al-Khrasani, David A. Karadi, Anna R. Galambos, Beata Sperlagh, E. Sylvester Vizi
Summary: This study investigated the effects of Phenylephrine (PE) on the release of noradrenaline (NA) and smooth muscle contractions. The results showed that PE significantly enhanced the release of NA independent of calcium ion concentration, and also had inhibitory effects on smooth muscle contractions induced by PE. This study highlights the indirect effects of PE and provides a possible mechanism for explaining its side effects.
NEUROCHEMICAL RESEARCH
(2022)
Article
Engineering, Environmental
Luisa Galgani, Isabel Gossmann, Barbara Scholz-Boettcher, Xiangtao Jiang, Zhanfei Liu, Lindsay Scheidemann, Cathleen Schlundt, Anja Engel
Summary: Understanding the residence times of plastic in the ocean is crucial for plastic pollution studies. Current observations show a mismatch between estimated plastic loads and actual floating plastics in the sea. Surveys of the water column are limited. Recent research proposes biofouling and degradation as the main processes for plastic removal. Plastic can affect the biogeochemical and microbial cycling of carbon and nutrients through organic matrices.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xingyu Zhang, Li Tang, Zhentao Zhang
Summary: ADAM10 and ADAM17 act as alpha-secretase to cleave membrane-anchored proteins, with lysosomal cysteine protease AEP playing a key role in their degradation. Knockout of AEP increases the content of ADAM10/17 in the brain, potentially implicating AEP-mediated degradation in the pathogenesis of Alzheimer's disease.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Guangyong Ma, Jun-ichirou Yasunaga, Kazuya Shimura, Keiko Takemoto, Miho Watanabe, Masayuki Amano, Hirotomo Nakata, Benquan Liu, Xiaorui Zuo, Masao Matsuoka
Summary: Retroviral antisense mRNAs are predominantly localized in the nucleus, functioning as long noncoding RNAs rather than mRNAs, and contributing to viral persistence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Qian He, Yue Wang, Quan Qiu, Yan Su, Hongxu Wei, Jiyue Li
Summary: This study found that people are more likely to feel happy when they are in degraded forests with low wind speeds, ample sunlight, tall vegetation, and high altitude. This suggests that policy makers should reassess the development value of degraded forests and pay attention to their nonmaterial services. Furthermore, policy makers could consider developing degraded forests as a type of infrastructure to promote people's mental well-being.
ECOSYSTEM HEALTH AND SUSTAINABILITY
(2023)
Article
Biochemistry & Molecular Biology
Lifang Hu, Chong Yin, Dong Chen, Zixiang Wu, Shujing Liang, Yu Zhang, Zizhan Huang, Shuyu Liu, Xia Xu, Zhihao Chen, Yi Zhang, Airong Qian
Summary: MACF1 plays a crucial role in osteoblast differentiation by modulating transcriptome dynamics and interacting with various proteins that inhibit osteoblast differentiation. MACF1 regulates cytoplasmic-nuclear localization of itself and other factors, while also controlling the expression of transcription factors driving osteoblast differentiation.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Ecology
Frederico R. Alves, Daniel Aguilera-Olivares, Mauricio Martins Rocha, Alberto Arab
Summary: Termites are important dung recyclers in ecosystems, especially in pastures.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Toshio Hattori, Hiroko Iwasaki-Hozumi, Gaowa Bai, Haorile Chagan-Yasutan, Ashwnini Shete, Elizabeth Freda Telan, Atsushi Takahashi, Yugo Ashino, Takashi Matsuba
Summary: During inflammation, osteopontin undergoes cleavage by various proteases to generate bioactive fragments affecting dendritic cell adhesion. Elevated levels of undefined osteopontin in plasma are associated with tuberculosis and COVID-19, reflecting distinct pathological conditions.
Article
Multidisciplinary Sciences
Julie Parenteau, Laurine Maignon, Melodie Berthoumieux, Mathieu Catala, Vanessa Gagnon, Sherif Abou Elela
Review
Cell Biology
Sherif Abou Elela, Xinhua Ji
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2019)
Article
Immunology
Pedro Miramon, Andrew W. Pountain, Ambro van Hoof, Michael C. Lorenz
INFECTION AND IMMUNITY
(2020)
Review
Genetics & Heredity
Julie Parenteau, Sherif Abou Elela
TRENDS IN GENETICS
(2019)
Article
Genetics & Heredity
Minseon Kim, Ambro van Hoof
Review
Cell Biology
Cyrielle Petibon, Mustafa Malik Ghulam, Mathieu Catala, Sherif Abou Elela
Summary: Ribosomal protein genes are highly expressed in most cell types and are essential for cell growth and proliferation. Regulation of these genes involves both general and gene-specific mechanisms, allowing the cell to coordinate ribosome production while maintaining functional specialization and diversity. Posttranscriptional regulatory events play a key role in fine-tuning the expression of ribosomal protein genes and controlling potential variation in ribosome functions.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Multidisciplinary Sciences
Jennifer E. Hurtig, Michelle A. Steiger, Vinay K. Nagarajan, Tao Li, Ti-Chun Chao, Kuang-Lei Tsai, Ambro van Hoof
Summary: Recent studies show that yeast TSEN cleaves a specific subset of mRNAs encoding mitochondrial proteins, with cleavage sites determined by sequence. The development of the comPARE bioinformatic approach enables the identification of these mRNA target sites more effectively.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Delong Zhou, Sonia Couture, Michelle S. Scott, Sherif Abou Elela
Summary: RBFOX2 controls splicing of transcripts involved in cell differentiation and development by interacting with various RNA-binding protein partners through different binding modes. These dynamic modes can bind distinct sets of transcripts at different positions relative to alternative splice sites, explaining the heterogeneous targets and outcomes of RBFOX2 splicing regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Gabrielle Deschamps-Francoeur, Sonia Couture, Sherif Abou-Elela, Michelle S. Scott
Summary: Box C/D small nucleolar RNAs (snoRNAs) play a role in guiding ribosomal RNA methylation and regulating non-ribosomal gene expression. The snoGloBe predictor enables the identification of snoRNA interactions and their regulatory function, showing enrichment near gene expression regulatory elements. The tool is also effective in discovering viral RNA targets, such as SARS-CoV-2 RNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Danny Bergeron, Hermes Paraqindes, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Laurence Faucher-Giguere, Philia Bouchard-Bourelle, Sherif Abou Elela, Frederic Catez, Virginie Marcel, Michelle S. Scott
Summary: snoDB is an interactive database providing up-to-date information on human small nucleolar RNAs (snoRNAs), including features, genomic location, conservation, host gene, snoRNA-RNA targets, and abundance. The second edition of snoDB introduces a new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs, with easy navigation between different rRNA versions used in literature and experimentally measured modification levels. Additional information including snoRNA motifs, secondary structure prediction, snoRNA-protein interactions, and expression data in various tissues and cell lines has been included to enhance functional probing of snoRNA biology. Version 2.0 also features updated identifiers, more external resource links, and duplicate entry resolution.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mustafa Malik Ghulam, Mathieu Catala, Gaspard Reulet, Michelle S. Scott, Sherif Abou Elela
Summary: We demonstrate that gene duplication in yeast serves as a stress-adaptation mechanism by modulating the global proteome through differential expression of ribosomal protein paralogs. This mechanism controls translation through differential acetylation of ribosomal proteins, favoring the translation of genes with short open reading frames under normal conditions and increasing translation of genes with long open reading frames after exposure to drugs. This study identifies a natural program where changing the ratio of proteins produced from duplicated genes modifies translation in response to drugs, regardless of ribosome number.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Kyra Kerkhofs, Jyoti Garg, Etienne Fafard-Couture, Sherif Abou Elela, Michelle S. Scott, Ronald E. Pearlman, Mark A. Bayfield
Summary: Studies have shown that the Tetrahymena thermophila protein Mlp1 plays a key role in La protein function, affecting pre-tRNA processing and stability of 3'-trailers when depleted. The short length of 3'-trailers in Tetrahymena thermophila compared to other eukaryotes, along with the evolution of 5'-leaders disfavoring pre-tRNA leader/trailer pairing, indicate a unique mechanism of tRNA processing in Tetrahymena thermophila associated with the variant architecture of Mlp1.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Nadirah S. Damseh, Ali N. Obeidat, Khondakar Sayef Ahammed, Motee Al-Ashhab, Motee Abu Awad, Ambro van Hoof
Summary: Pontocerebellar hypoplasia (PCH) is a rare neurodegenerative disorder characterized by various clinical features. A 3-month-old female with PCH and additional clinical features, including dilated cardiomyopathy, was reported in this study. Whole-exome sequencing revealed a novel homozygous missense variant in the EXOSC1 gene, which has been shown to cause defects in RNA exosome function.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Genetics & Heredity
Jennifer E. Hurtig, Ambro van Hoof
Summary: Through yeast genetics, it is discovered that TSEN not only participates in tRNA splicing but also has other functions, including degradation of a subset of mRNA encoding mitochondrial proteins and an unknown essential function. Overexpression of SEN54 can suppress sen2 mutants, indicating its general suppressive effect on sen2, regardless of tRNA-dependent or tRNA-independent functions. Mutations in the intron-debranching enzyme Dbr1 can also serve as tRNA splicing-independent suppressors. These findings provide insights into the essential function(s) of TSEN.
Article
Biochemistry & Molecular Biology
Laurence Faucher-Giguere, Audrey Roy, Gabrielle Deschamps-Francoeur, Sonia Couture, Ryan M. Nottingham, Alan M. Lambowitz, Michelle S. Scott, Sherif Abou Elela
Summary: This study accurately surveyed the abundance of snoRNAs in ovarian cancer tissues using a sensitive sequencing technique. Several specific snoRNAs were identified, which may promote tumor aggressiveness by inducing rRNA modification and synthesis.