Article
Biochemistry & Molecular Biology
Xiao Li, Janice M. Zengel, Lasse Lindahl
Summary: This article describes a novel pathway to the long 5.8S rRNA formation via degradation of ITS1 from its 5' end by exonuclease Xrn1. Mutations in RNase MRP lead to an increase in the accumulation of long 5.8S rRNA relative to short 5.8S rRNA, even when the A3 site is deleted. The link between RNase MRP and 5.8S 5' end formation may involve cleavage at unknown sites elsewhere in pre-rRNA or other RNA molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Toshinori Oozeki, Tadashi Nakai, Kazuki Kozakai, Kazuki Okamoto, Shun'ichi Kuroda, Kazuo Kobayashi, Katsuyuki Tanizawa, Toshihide Okajima
Summary: In this study, a flavoprotein monooxygenase essential for the biosynthesis of cysteine tryptophylquinone (CTQ) cofactor is characterized both functionally and structurally. The diversity in tryptophylquinone-generating systems suggests convergent evolution of tryptophan-derived cofactors in various proteins.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Bing Ma, Hui Liu, Zhi-hui Xiu, Huan-huan Yang, Hongqiu Wang, Yong Wang, Bao-Cai Tan
Summary: Ribosome biogenesis in plants is not well understood. This study identified DEK58 as a crucial protein involved in seed development in maize. DEK58 interacts with other proteins and plays a role in the early stage of ribosome biogenesis.
Article
Plant Sciences
Monika Zakrzewska-Placzek, Anna Golisz-Mocydlarz, Michal Krzyszton, Justyna Piotrowska, Malgorzata Lichocka, Joanna Kufel
Summary: This study demonstrates the involvement of AtNOL12 in rRNA biogenesis and its correlation with stress response in plants. The absence of AtNOL12 alters the expression of ribosomal protein and ribosome biogenesis genes, potentially impacting ribosome function.
Article
Biochemistry & Molecular Biology
Mitsuru Okuwaki, Shoko Saito, Hiroko Hirawake-Mogi, Kyosuke Nagata
Summary: This study revealed that the nucleolar localization of NPM1 and the large ribosomal subunit precursors are mutually dependent. NPM1 plays a crucial role in maintaining the structure of large ribosomal subunits and the accumulation of late processing machinery in the nucleolus.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Microbiology
Fangchao Song, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin
Summary: In this study, a direct PCR method was evaluated as a cost-effective and time-saving alternative to traditional DNA extraction methods for analyzing microbial communities. The direct PCR method showed comparable efficiency to the conventional DNeasy PowerSoil protocol, with higher efficiency for extracting gDNA from Gram-negative strains. This method is significantly less expensive and faster, making it a potential solution for high-throughput large-scale bacterial community analysis.
Article
Biochemistry & Molecular Biology
Baizhu Chen, Wei Kang, Jing Sun, Runtao Zhu, Yue Yu, Aiguo Xia, Mei Yu, Meng Wang, Jinyu Han, Yixuan Chen, Lijun Teng, Qiong Tian, Yin Yu, Guanglin Li, Lingchong You, Zhiyuan Liu, Zhuojun Dai
Summary: The study successfully demonstrated the programmed self-assembly of bacterial populations using engineered adhesion, resulting in the development of versatile, programmable, self-healing living materials. The materials have fast recovery capabilities and can be used to create wearable sensors for detecting bio signals.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Julia S. P. Mawer, Jennifer Massen, Christina Reichert, Niklas Grabenhorst, Constantine Mylonas, Peter Tessarz
Summary: Ribosome biogenesis is a complex cellular process that involves integration of extracellular cues, such as metabolic state and intracellular signaling, transcriptional regulation, and chromatin accessibility at the ribosomal DNA. The recently identified histone modification, methylation of H2AQ105 (H2AQ105me), plays a key role in this process, dependent on the mTor signaling pathway and acetylation of histone H3. The ribonucleoprotein Nhp2 acts as an epigenetic reader of this modification, bridging rDNA chromatin with components of the small subunit processome to coordinate transcription of rRNA with its post-transcriptional processing.
Article
Biochemistry & Molecular Biology
Carson J. Bryant, Mason A. McCool, Laura Abriola, Yulia Surovtseva, Susan J. Baserga
Summary: Studies of nucleolar function regulation are important for understanding the basic biology of ribosome biogenesis and developing therapeutics for cancer and ribosomopathies. Existing high-throughput assays indirectly identify drugs affecting ribosome biogenesis based on morphological changes in the nucleolus, but a more direct assay is needed. We report a high-throughput assay for nucleolar function that quantifies nucleolar rRNA biogenesis using 5-ethynyl uridine (5-EU) and nucleolar protein fibrillarin (FBL). This new method enables closer study of ribosome biogenesis in health and disease.
Article
Biochemistry & Molecular Biology
Leonid Anikin, Dimitri G. Pestov
Summary: Aminoacridines, historically used as antiseptic and antiparasitic agents, could be repurposed for therapeutic use and new drug development. In this study, the effects of 9-aminoacridine on pre-rRNA metabolism in mammalian cells were investigated. The results showed that 9-aminoacridine inhibits both pre-rRNA transcription and processing, leading to the disruption of ribosome biogenesis. The ability of 9-aminoacridine to bind to RNA in vitro suggests its potential as a new ribosome biogenesis inhibitor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Jie Cui, Yamin Zhang, Xiaoyue Ren, Lei Jin, Hongyi Zhang
Summary: TBX1 is highly expressed in PCa and is positively correlated with disease progression and survival. By inhibiting cell proliferation and promoting cell cycle arrest in PCa, TBX1 may exert its function through influencing rRNA gene transcription.
FRONTIERS IN ONCOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Le Wang, Wenfu Zheng, Sixiang Li, Leni Zhong, Xingyu Jiang
Summary: This study presents the modification of gold nanoparticles with aminophenol, which demonstrates a broad spectrum of antibacterial effects and strong efficacy against multidrug-resistant bacteria. The mechanisms of action include damaging bacterial cell walls and inhibiting bacterial protein synthesis. In vivo experiments also show promising results in treating abdominal bacterial infections.
Article
Plant Sciences
Zhenjing Ren, Kaijian Fan, Sihan Zhen, Jie Zhang, Yan Liu, Junjie Fu, Chunlai Qi, Qianhan Wei, Yao Du, Wurinile Tatar, Xiaofeng Zhang, Guoying Wang, Allan G. Rasmusson, Jianhua Wang, Yunjun Liu
Summary: The maize gene SMK11 encodes a mitochondria-localized tetratricopeptide repeat protein, which plays critical roles in the assembly and activity of mitochondrial complex IV, and is essential for seed development.
Article
Microbiology
Natividad Ruiz, Rebecca M. Davis, Sujeet Kumar
Summary: The process of transporting phospholipids to the outer membrane in Gram-negative bacteria, an essential step in envelope biogenesis, remains unclear. Through studying the AsmA-like clan in Escherichia coli, it was found that YhdP and its homologs TamB and YdbH play important roles in maintaining lipid homeostasis and growth in the outer membrane. These proteins are proposed to be the long-sought-after phospholipid transporters essential for outer membrane biogenesis.
Article
Oncology
Zhiyong Liu, Yanan Pang, Yin Jia, Qin Qin, Rui Wang, Wei Li, Jie Jing, Haidong Liu, Shanrong Liu
Summary: This study found that SNORA23 regulates ribosome biogenesis in hepatocellular carcinoma (HCC) by impairing the 2'-O-ribose methylation of 28S rRNA. SNORA23 inhibits the proliferation, migration, and invasion of HCC cells in vitro and in vivo. It is regulated by the PI3K/Akt/mTOR signaling pathway and inhibits the phosphorylation of 4E binding protein 1.
CANCER BIOLOGY & MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Manasses Jora, Kayla Borland, Scott Abernathy, Ruoxia Zhao, Melissa Kelley, Stefanie Kellner, Balasubrahmanyam Addepalli, Patrick A. Limbach
Summary: LC-MS/MS is currently the leading technique for studying RNA and its modifications. The discovery of a non-natural ribonucleoside in tRNA hydrolysate highlights the importance of minimizing artifacts during sample preparation. Optimizing digestion conditions can lead to more accurate detection of new RNA modifications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Yasemin Yoluc, Gregor Ammann, Pierre Barraud, Manasses Jora, Patrick A. Limbach, Yuri Motorin, Virginie Marchand, Carine Tisne, Kayla Borland, Stefanie Kellner
Summary: Organisms invest significant energy in introducing RNA modifications into transcripts, with instrumental analysis focusing on modified residues to reveal the function of epitranscriptomic marks. Recent advances and breakthroughs in the study of the epitranscriptome have been made through NMR spectroscopy, sequencing, and mass spectrometry.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Kai Papenfort, Sarah A. Woodson, Ruth A. Schmitz, Wade C. Winkler
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Michel Fasnacht, Stefano Gallo, Puneet Sharma, Maximilian Himmelstoss, Patrick A. Limbach, Jessica Willi, Norbert Polacek
Summary: Post-transcriptional modifications of ribosomal RNAs, such as the ho(5)C2501 modification, play a crucial role in regulating protein biosynthesis in bacteria. Studies show that high levels of ho(5)C2501 reduce protein biosynthesis in E. coli but are beneficial for the bacteria in adapting to oxidative stress, especially in the presence of hydrogen peroxide. This unique modification provides functional insights into ribosome functions and bacterial growth under oxidative stress.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Melissa Kelley, Melissa Uhran, Cassandra Herbert, George Yoshida, Emmarie R. Watts, Patrick A. Limbach, Joshua B. Benoit
Summary: The modification of tRNA in mosquitoes, especially in females, may play a critical role in reproduction and could be a potential target for controlling fertility.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Melissa Kelley, Mellie June Paulines, George Yoshida, Ryan Myers, Manasses Jora, Joel P. Levoy, Balasubrahmanyam Addepalli, Joshua B. Benoit, Patrick A. Limbach
Summary: This study focuses on the modifications and stability of tRNAs in the fungus C. neoformans, which is known for its ability to withstand oxidative conditions. The results show that the modifications and transcripts of tRNAs are minimally affected regardless of environmental conditions. The study also proposes a theoretical explanation for the rapid adaptation of C. neoformans to oxidative environments.
Article
Multidisciplinary Sciences
Luigi D'Ascenzo, Anna M. Popova, Scott Abernathy, Kai Sheng, Patrick A. Limbach, James R. Williamson
Summary: This article introduces an automated software tool, Pytheas, for the analysis of modified RNA using mass spectrometry. Pytheas features flexible handling of isotope labeling and RNA modifications, with statistical validation of false discovery rate using sequence decoys. It is a valuable tool for bottom-up mass spectrometry characterization of diverse RNA sequences, with applications in the biology of stable RNAs, as well as quality control of RNA therapeutics and mRNA vaccines.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jorjethe Roca, Andrew Santiago-Frangos, Sarah A. Woodson
Summary: The pairwise interactions between bacterial sRNAs and Hfq determine whether the sRNAs are actively exchanged or stably coexist on the shared protein.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Priti Thakur, Jowad Atway, Patrick A. Limbach, Balasubrahmanyam Addepalli
Summary: Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. In this study, the cleavage specificity and efficiency of ribonuclease MC1 and cusativin were investigated using a customized RNA sequence. The results showed that both enzymes exhibited different preferences for dinucleotide combinations, and the observed substrate specificity was supported by molecular docking analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Manasses Jora, Daniel Corcoran, Gwenn G. Parungao, Peter A. Lobue, Luiz F. L. Oliveira, George Stan, Balasubrahmanyam Addepalli, Patrick A. Limbach
Summary: This study demonstrates the capability of using higher-energy collisional dissociation (HCD) spectra in combination with spectral matching for the semi-automated characterization of ribonucleosides. Analysis of tRNA hydrolysates using systematic spectral matching has provided evidence for the existence of novel ribonucleoside modifications. This approach has the potential to simplify the characterization of unknown modified ribonucleosides and accelerate discoveries in the epitranscriptome.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Samantha H. Sarni, Jorjethe Roca, Chen Du, Mengxuan Jia, Hantian Li, Ana Damjanovic, Ewelina M. Malecka, Vicki H. Wysocki, Sarah A. Woodson
Summary: RNA-binding protein Hfq stabilizes its hexamer through a network of intrinsically disordered interactions between the core and flexible C-terminal domains (CTDs). This network is perturbed by RNA binding, but partially compensated by RNA interactions with multiple surfaces of Hfq.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Margaret L. Rodgers, Brett O'Brien, Sarah A. Woodson
Summary: sRNPs play key roles in guiding the folding, modification, and splicing of nascent precursor RNAs during transcription. However, the rapid co-transcriptional folding of RNA can hinder the recognition and regulation of sRNP binding sites. In this study, the binding of Hfq•DsrA sRNPs to rpoS transcripts was examined using the single-molecule co-localization co-transcriptional assembly (smCoCoA) technique. It was found that Hfq•DsrA samples the mRNA before the transcription of the target site, preparing it for base pairing with DsrA. Furthermore, it was observed that Hfq•DsrA often binds to the mRNA close to RNA polymerase (RNAP) during the synthesis of the target site. This suggests that targeting transcripts near RNAP allows sRNPs to capture the site before the RNA folds, providing a kinetic advantage in recognition and regulation.
Meeting Abstract
Zoology
M. Kelley, M. Uhran, C. Herbert, G. Yoshida, P. A. Limbach, J. B. Benoit
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yuan Lou, Sarah A. Woodson
Summary: This study shows that self-cleavage of the glmS ribozyme riboswitch can occur during transcription before the ribozyme is fully synthesized. Co-transcriptional folding of the RNA allows the ribozyme catalytic core to react without the downstream stability domain. Slow sequential folding promotes the formation of the native core structure. Ribozyme self-cleavage at an early stage of transcription is important for the regulation of glmS in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Jana Jeschke, Evelyne Collignon, Clemence Al Wardi, Mohammad Krayem, Martin Bizet, Yan Jia, Soizic Garaud, Zena Wimana, Emilie Calonne, Bouchra Hassabi, Renato Morandini, Rachel Deplus, Pascale Putmans, Gaurav Dube, Nitesh Kumar Singh, Alexander Koch, Kateryna Shostak, Lara Rizzotto, Robert L. Ross, Christine Desmedt, Yacine Bareche, Francoise Rothe, Jacqueline Lehmann-Che, Martine Duterque-Coquillaud, Xavier Leroy, Gerben Menschaert, Luis Teixeira, Mingzhou Guo, Patrick A. Limbach, Pierre Close, Alain Chariot, Eleonora Leucci, Ghanem Ghanem, Bi-Feng Yuan, Karen Willard-Gallo, Christos Sotiriou, Jean-Christophe Marine, Francois Fuks
Summary: The study found that downregulation of the FTO m(6)A RNA demethylase in epithelial cancers leads to increased invasion, metastasis, and worse clinical outcomes. Experimental evidence showed that FTO silencing promotes cancer growth, cell motility, and invasion, while FTO pharmacological inhibition favors tumorigenesis.