Article
Biochemistry & Molecular Biology
Yuhei Chadani, Nobuyuki Sugata, Tatsuya Niwa, Yosuke Ito, Shintaro Iwasaki, Hideki Taguchi
Summary: Translation elongation is essential for organisms to produce their proteomes, but there is a risk of elongation abortion due to sequences like intrinsic ribosome destabilization (IRD) sequences. Most potential IRD sequences in the middle of open reading frames remain hidden and do not interrupt translation, as the nascent polypeptide itself acts as a bridge in the ribosome, protecting it from dissociation. This inherent ability of nascent polypeptide products ensures elongation continuity.
Article
Multidisciplinary Sciences
Kevin C. Stein, Fabian Morales-Polanco, Joris van der Lienden, T. Kelly Rainbolt, Judith Frydman
Summary: Ageing is accompanied by a decline in cellular proteostasis. Altered translational efficiency during ageing could help drive the collapse of proteostasis, leading to systemic decline.
Review
Microbiology
Lorenzo Eugenio Leiva, Victor Zegarra, Gert Bange, Michael Ibba
Summary: Nucleotides are essential for biological processes in the cell, playing key roles in molecular biology and regulating metabolic pathways. They are dynamic, interact with each other, and provide feedback to the cell's metabolic state, adapting to environmental and growth challenges. Intracellular nucleotides fine-tune the activity of RNA polymerase, synthesis of tRNAs, mRNA translation, and assembly of ribosomes involved in protein synthesis. The ribosome acts as a molecular hub where nucleotides encounter and regulate the cell's state.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Matthew L. Kraushar, Ferdinand Krupp, Dermot Harnett, Paul Turko, Mateusz C. Ambrozkiewicz, Thiemo Sprink, Koshi Imami, Manuel Guennigmann, Ulrike Zinnall, Carlos H. Vieira-Vieira, Theres Schaub, Agnieszka Muenster-Wandowski, Joerg Buerger, Ekaterina Borisova, Hiroshi Yamamoto, Mladen-Roko Rasin, Uwe Ohler, Dieter Beule, Thorsten Mielke, Victor Tarabykin, Markus Landthaler, Guenter Kramer, Imre Vida, Matthias Selbach, Christian M. T. Spahn
Summary: This study explores the architecture of ribosomes in the developing nervous system and identifies Ebp1 as a crucial factor in protein synthesis, playing a key role in cell morphology and the synthesis of membrane-targeted cell adhesion molecules. Ebp1 regulates ribosome occupancy of specific codons during different stages of protein synthesis in the neocortex, highlighting its importance in neuronal development.
Review
Microbiology
Xiao Wang, Jie Zhu, Da Zhang, Guangqing Liu
Summary: Viruses are intracellular parasites that rely on host cellular functions to reproduce. They manipulate ribosomes to synthesize their own proteins and regulate ribosome production and assembly to promote viral protein synthesis and inhibit host antiviral protein synthesis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Aleksandar Radakovic, Saurja DasGupta, Tom H. Wright, Harry R. M. Aitken, Jack W. Szostak
Summary: Research shows that aminoacylated RNAs can assemble into chimeric amino acid-RNA polymers with active ribozyme function under template guidance, potentially introducing new functionalities in ribozyme catalysis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Fluids & Plasmas
Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close, Liesbet Geris
Summary: This study introduces a basic electrostatic model of the ribosome exit tunnel, revealing the interaction mechanism between water molecules and nascent proteins inside the tunnel, as well as the impact of tunnel wall components and protein protrusions on the electrostatic potential distribution. The model also quantitatively explains the effects of charged amino acid residues progressing through the tunnel and provides predictions for the forces acting on the peptide chain. Through this model, experimental data point measurements are linked to the local structural chemistry of the inner wall, shape, and size of the tunnel.
Review
Microbiology
Ekaterina Samatova, Jan Daberger, Marija Liutkute, Marina V. Rodnina
Summary: Ribosome pausing affects translational efficiency and protein folding, as well as the quality of newly synthesized proteins. It emerges as an important factor in regulatory programs that maintain the quality of the proteome and integrate cellular and environmental cues into regulatory circuits of the cell.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Olga A. Postnikova, Sheetal Uppal, Weiliang Huang, Maureen A. Kane, Rafael Villasmil, Igor B. Rogozin, Eugenia Poliakov, T. Michael Redmond
Summary: The SARS-CoV-2 Spike glycoprotein has acquired a unique insert sequence that could affect virus spread and infection mechanisms, prompting further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Paleerath Peerapen, Chanettee Chanthick, Visith Thongboonkerd
Summary: Caffeine and trigonelline, the major bioactive compounds in coffee, have hepatoprotective effects but their molecular mechanisms are unclear. Through proteomic and bioinformatic analyses, we identified altered proteins and revealed common and unique molecular mechanisms of caffeine and trigonelline in human hepatocytes. Ribosomal and translation regulatory proteins were found to play a key role, and induction of translational processes is a shared mechanism. This research provides insights for future clinical applications.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Review
Biochemistry & Molecular Biology
Sarah C. Miller, Clinton C. MacDonald, Morgana K. Kellogg, Zemfira N. Karamysheva, Andrey L. Karamyshev
Summary: Ribosomal heterogeneity exists within and between cells, and exhibits specific changes in response to developmental stages and environmental stimuli. These changes regulate the translation of specific groups of genes by altering ribosomal affinity for certain mRNAs or the folding of nascent polypeptides. The identification of specialized ribosomes relies on evidence such as different ribosomal protein composition or modifications to RNA and/or protein, resulting in physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their implications in several human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Yun-Ting Tseng, Yu-Cheng Sung, Ching-Yu Liu, Kai-Yin Lo
Summary: This study shows that eIF4G1 is directly involved in the biogenesis of the 60S ribosomal subunit in Saccharomyces cerevisiae cells. It plays a crucial role in facilitating PET maturation and 27S processing.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Naoyuki Tajima, Toshitaka Kumagai, Yutaka Saito, Tomoshi Kameda
Summary: The relationship between translation efficiency and sequence features varies across organisms, reflecting their taxonomy. The codon adaptation index shows high correlation in all analyzed organisms.
Article
Multidisciplinary Sciences
Chetana Baliga, Tyler J. Brown, Tanja Florin, Sarah Colon, Vallari Shah, Kornelia J. Skowron, Amira Kefi, Teresa Szal, Dorota Klepacki, Terry W. Moore, Nora Vazquez-Laslop, Alexander S. Mankin
Summary: Apidaecin is an 18-amino-acid proline-rich antibacterial peptide produced by bees that inhibits translation termination by invading the ribosome's nascent peptide exit tunnel. By analyzing the activity of different mutants with single-amino-acid substitutions, researchers were able to map critical interactions with the ribosome, tRNA, and release factors, as well as identify a segment of Api that tolerates amino acid substitutions for potential pharmacological improvement.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Qiutao Xu, Yijie Wang, Yaping Yue, Zhengting Chen, Dao-Xiu Zhou, Yu Zhao
Summary: This article has been withdrawn due to an error, and the definitive version is published under DOI.
Article
Biochemistry & Molecular Biology
Marlon G. Lawrence, Md Shamsuzzaman, Maithri Kondopaka, Clarence Pascual, Janice M. Zengel, Lasse Lindahl
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Itai Wekselman, Ella Zimmerman, Chen Davidovich, Matthew Belousoff, Donna Matzov, Miri Krupkin, Haim Rozenberg, Anat Bashan, Gilgi Friedlander, Jette Kjeldgaard, Hanne Ingmer, Lasse Lindahl, Janice M. Zengel, Ada Yonath
Article
Biochemistry & Molecular Biology
Nenad Ban, Roland Beckmann, Jamie H. D. Cate, Jonathan D. Dinman, Francois Dragon, Steven R. Ellis, Denis L. J. Lafontaine, Lasse Lindahl, Anders Liljas, Jeffrey M. Lipton, Michael A. McAlear, Peter B. Moore, Harry F. Noller, Joaquin Ortega, Vikram Govind Panse, V. Ramakrishnan, Christian M. T. Spahn, Thomas A. Steitz, Marek Tchorzewski, David Tollervey, Alan J. Warren, James R. Williamson, Daniel Wilson, Ada Yonath, Marat Yusupov
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2014)
Article
Cell Biology
Mamata Thapa, Ananth Bommakanti, Md Shamsuzzaman, Brian Gregory, Leigh Samsel, Janice M. Zengel, Lasse Lindahl
MOLECULAR BIOLOGY OF THE CELL
(2013)
Article
Multidisciplinary Sciences
Md Shamsuzzaman, Ananth Bommakanti, Aviva Zapinsky, Nusrat Rahman, Clarence Pascual, Lasse Lindahl
Article
Biochemistry & Molecular Biology
Ananth S. Bommakanti, Lasse Lindahl, Janice M. Zengel
Article
Biochemistry & Molecular Biology
Lasse Lindahl, Ananth Bommankanti, Xing Li, Lauren Hayden, Adrienne Jones, Miriam Khan, Tolulope Oni, Janice M. Zengel
Article
Biochemistry & Molecular Biology
Jesse M. Fox, Rebekah L. Rashford, Lasse Lindahl
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Multidisciplinary Sciences
Nusrat Rahman, Md Shamsuzzaman, Lasse Lindahl
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
Microbiology
Md Shamsuzzaman, Nusrat Rahman, Brian Gregory, Ananth Bommakanti, Janice M. Zengel, Vincent M. Bruno, Lasse Lindahl
Summary: Mutations in genes for ribosomal proteins or assembly factors result in cell stress and altered cell fate, leading to congenital diseases known as ribosomopathies. However, these diseases are not solely caused by reduced protein synthesis capacity. The mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differently.
Correction
Biology
Brian Gregory, Nusrat Rahman, Ananth Bommakanti, Md Shamsuzzaman, Mamata Thapa, Alana Lescure, Janice M. Zengel, Lasse Lindahl
LIFE SCIENCE ALLIANCE
(2019)
Article
Biology
Brian Gregory, Nusrat Rahman, Ananth Bommakanti, Md Shamsuzzaman, Mamata Thapa, Alana Lescure, Janice M. Zengel, Lasse Lindahl
LIFE SCIENCE ALLIANCE
(2019)
Article
Biochemistry & Molecular Biology
Sephorah Zaman, Megan Fitzpatrick, Lasse Lindahl, Janice Zengel
MOLECULAR MICROBIOLOGY
(2007)