Article
Multidisciplinary Sciences
Sohail Khoshnevis, R. Elizabeth Dreggors-Walker, Virginie Marchand, Yuri Motorin, Homa Ghalei
Summary: Protein synthesis by ribosomes is crucial for gene expression in cells, and 2'-O-methylation is a common modification on ribosomal RNAs. This study reveals that changes in the biogenesis of snoRNPs, which guide 2'-O-methylation, lead to the production of ribosomes with distinct translational properties. The hypo-2'-O-methylated ribosomes show translational defects and affect ribosome dynamics and ligand binding. This highlights the importance of 2'-O-methylation in regulating cellular translation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Daria D. Nikolaeva, Mikhail S. Gelfand, Sofya K. Garushyants
Summary: The ribosome, responsible for protein biosynthesis, is highly conserved in structure and composition across species. However, some bacteria may lack certain ribosomal proteins, especially in organisms with significantly reduced genomes. The large subunit of the ribosome shows less conservation in protein composition compared to the small subunit.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Chemistry, Multidisciplinary
Hao-Yuan Wang, Haojun Yang, Mikael Holm, Keely Oltion, Harrison Tom, Amjad Ayad Qatran Al-Khdhairawi, Jean-Frederic F. Weber, Scott C. Blanchard, Davide Ruggero, Jack Taunton
Summary: Ternatin-family cyclic peptides inhibit protein synthesis by targeting eukaryotic elongation factor-1 alpha. The synthetic SR-A3 showed enhanced residence time and rebinding kinetics compared to SS-A3, both in vitro and in cells. Thrice-weekly dosing with SR-A3 reduced tumor burden and increased survival in a mouse lymphoma model. These findings demonstrate the potential of SR-A3 as a cancer therapeutic and suggest an evolutionary mechanism for enhancing cyclic peptide binding kinetics via stereospecific side-chain hydroxylation.
Article
Biochemical Research Methods
Laurel F. Kinman, Barrett M. Powell, Ellen D. Zhong, Bonnie Berger, Joseph H. Davis
Summary: This paper introduces a machine learning system called CryoDRGN for reconstructing proteins and protein complexes from single-particle cryo-EM data. The system utilizes a deep generative model to generate 3D density maps and provides methods for analyzing and interpreting the resulting ensemble. However, interpreting the ensemble is still a challenge.
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
Oncology
Jurandir Cruz, Bernardo Lemos
Summary: In this study, the authors discuss the regulatory mechanisms of post-transcriptional and post-translational modifications on ribosomal function, as well as their impact on cellular metabolism, replication control, and senescence. The research findings suggest that disruptions in these modifications can impair ribosome biogenesis and function, thus affecting protein synthesis related to carcinogenesis and senescence.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Clinical Neurology
Doriana Misceo, Lisa Lirussi, Petter Stromme, Dulika Sumathipala, Andrea Guerin, Nicole Wolf, Andres Server, Maria Stensland, Bjorn Dalhus, Aslihan Tolun, Hester Y. Kroes, Tuula A. Nyman, Hilde L. Nilsen, Eirik Frengen
Summary: This study reports two patients with leukodystrophy and cerebellar atrophy caused by defective POLR1A. Experiments in patient fibroblasts reveal abnormalities in nucleolar homeostasis, protein homeostasis, and endoplasmic reticulum stress responses, providing new insights into the pathogenesis of POLR1A-related leukodystrophy.
Article
Biochemistry & Molecular Biology
Minju Joo, Ji-Hyun Yeom, Younkyung Choi, Hyeon Jun, Wooseok Song, Hyun-Lee Kim, Kangseok Lee, Eunkyoung Shin
Summary: The ribosome, once considered homogeneous, is now known to be highly heterogeneous and plays specialized roles in translational regulation. This review provides an overview of the current understanding of ribosome heterogeneity and their specialized functions, as well as discussions on specific translation systems that utilize orthogonal ribosomes.
Article
Biology
Elke De Zitter, Nicolas Coquelle, Paula Oeser, Thomas R. M. Barends, Jacques-Philippe Colletier
Summary: Xtrapol8 is a program for automatically extracting structural information of low occupancy states, accelerating and facilitating data processing in kinetic, time-resolved and ligand-based crystallographic studies.
COMMUNICATIONS BIOLOGY
(2022)
Review
Rheumatology
Guus G. H. van den Akker, Marjolein M. J. Caron, Mandy J. Peffers, Tim J. M. Welting
Summary: This review discusses the role of the ribosome in the pathogenesis of osteoarthritis, highlighting the potential importance of ribosome aberrations in the development of the disease. The authors propose the hypothesis of an "acquired ribosomopathy" in osteoarthritis, suggesting novel opportunities for disease-modifying treatments.
CURRENT OPINION IN RHEUMATOLOGY
(2022)
Article
Chemistry, Physical
Arthur Voronin, Alexander Schug
Summary: Despite significant progress in experimental techniques, protein structure determination remains a challenging task. Computer simulations are often used to complement or interpret experimental data, with many methods providing highly accurate protein structure models. Research focuses on selecting representative members or ensembles from computationally generated structures.
JOURNAL OF CHEMICAL PHYSICS
(2022)
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
Biochemistry & Molecular Biology
Chieh-Hsin Chen, Yi-Ting Chou, Ya-Wen Yang, Kai-Yin Lo
Summary: High dose copper treatment blocks ribosome biogenesis, leading to nucleolar stress and cell death.
Article
Plant Sciences
Zi-Yuan Wang, Wan-Tong Qu, Tong Mei, Nan Zhang, Nai-Ying Yang, Xiao-Feng Xu, Hai-Bo Xiong, Zhong-Nan Yang, Qing-Bo Yu
Summary: This study further analyzed the function of AtRsmD in chloroplast development and photosynthesis, revealing its distinct regulatory roles in chloroplast translation.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Hong-Yeoul Ryu
Summary: Ribosomes are essential for protein production in all living organisms. The process of ribosome biogenesis involves multiple steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. This review summarizes the current studies and recent progress on how SUMOylation regulates ribosome biogenesis.
Article
Multidisciplinary Sciences
Anna B. Loveland, Gabriel Demo, Nikolaus Grigorieff, Andrei A. Korostelev
Article
Multidisciplinary Sciences
Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, Andrei A. Korostelev
SCIENTIFIC REPORTS
(2017)
Article
Biology
Gabriel Demo, Egor Svidritskiy, Rohini Madireddy, Ruben Diaz-Avalos, Timothy Grant, Nikolaus Grigorieff, Duncan Sousa, Andrei A. Korostelev
Review
Biochemistry & Molecular Biology
Egor Svidritskiy, Gabriel Demo, Andrei A. Korostelev
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Egor Svidritskiy, Andrei A. Korostelev
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Biochemical Research Methods
Anna B. Loveland, Andrei A. Korostelev
Article
Biochemistry & Molecular Biology
Egor Svidritskiy, Andrei A. Korostelev
Article
Genetics & Heredity
Jacob C. Ulirsch, Jeffrey M. Verboon, Shideh Kazerounian, Michael H. Guo, Daniel Yuan, Leif S. Ludwig, Robert E. Handsaker, Nour J. Abdulhay, Claudia Fiorini, Giulio Genovese, Elaine T. Lim, Aaron Cheng, Beryl B. Cummings, Katherine R. Chao, Alan H. Beggs, Casie A. Genetti, Colin A. Sieff, Peter E. Newburger, Edyta Niewiadomska, Michal Matysiak, Adrianna Vlachos, Jeffrey M. Lipton, Eva Atsidaftos, Bertil Glader, Anupama Narla, Pierre-Emmanuel Gleizes, Marie-Francoise O'Donohue, Nathalie Montel-Lehry, David J. Amor, Steven A. McCarroll, Anne H. O'Donnell-Luria, Namrata Gupta, Stacey B. Gabriel, Daniel G. MacArthur, Eric S. Lander, Monkol Lek, Lydie Da Costa, David G. Nathan, Andrei K. Korostelev, Ron Do, Vijay G. Sankaran, Hanna T. Gazda
AMERICAN JOURNAL OF HUMAN GENETICS
(2018)
Article
Biology
Egor Svidritskiy, Gabriel Demo, Anna B. Loveland, Chen Xu, Andrei A. Korostelev
Article
Biology
Chen Bao, Sarah Loerch, Clarence Ling, Andrei A. Korostelev, Nikolaus Grigorieff, Dmitri N. Ermolenko
Article
Multidisciplinary Sciences
Anna B. Loveland, Gabriel Demo, Andrei A. Korostelev
Article
Multidisciplinary Sciences
Hung-Lun Hsu, Alexander Brown, Anna B. Loveland, Anoushka Lotun, Meiyu Xu, Li Luo, Guangchao Xu, Jia Li, Lingzhi Ren, Qin Su, Dominic J. Gessler, Yuquan Wei, Phillip W. L. Tai, Andrei A. Korostelev, Guangping Gao
NATURE COMMUNICATIONS
(2020)
Review
Biochemistry & Molecular Biology
Andrei A. Korostelev
Summary: Studies have shown significant similarities between translation termination and ribosome rescue mechanisms at the molecular level, both of which rely on the dynamic nature of ribosomes, highlighting the active role of ribosomes in all translation steps.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Multidisciplinary Sciences
Gabriel Demo, Howard B. Gamper, Anna B. Loveland, Isao Masuda, Christine E. Carbone, Egor Svidritskiy, Ya-Ming Hou, Andrei A. Korostelev
Summary: The study found that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Christine E. Carbone, Gabriel Demo, Rohini Madireddy, Egor Svidritskiy, Andrei A. Korostelev
NATURE COMMUNICATIONS
(2020)