Article
Biochemistry & Molecular Biology
Paul Powell, Usha Bhardwaj, Dixie Goss
Summary: This study identifies secondary structures that selectively interact with eIF3 and explores its role in translation initiation of BYDV. The findings propose a new model for BYDV translation initiation and expand the known functionality of eIF3.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Chengzhi Xu, Yupeng Shen, Yong Shi, Ming Zhang, Liang Zhou
Summary: This study reveals the role of EIF3B in head and neck squamous cell carcinoma (HNSCC) and identifies its promotion of CEBPB translation and IL6R expression. These findings provide important insights into the molecular basis and pathogenesis of HNSCC.
CANCER CELL INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Cristina Remes, Anas Khawaja, Sarah F. Pearce, Adam M. Dinan, Shreekara Gopalakrishna, Miriam Cipullo, Vasileios Kyriakidis, Jingdian Zhang, Xaquin Castro Dopico, Olessya Yukhnovets, Ilian Atanassov, Andrew E. Firth, Barry Cooperman, Joanna Rorbach
Summary: The detailed mechanism of mitochondrial translation in human mitochondria remains unclear. This study reveals that leaderless mRNA transcripts can be directly loaded onto assembled 55S mitochondrial ribosomes in human mitochondria, but not onto the small subunit, and this process requires initiator fMet-tRNA(Met) binding. Furthermore, this study demonstrates that mtIF3 is not involved in translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the bicistronic ATP8/ATP6 transcript. These findings provide insights into the evolutionary divergence of mitochondrial translation and enhance our understanding of a critical process in eukaryotic metabolism.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Madhurima Datta, Maalavika Pillai, Mamata Jayant Modak, Aivar Liiv, Faisal Tarique Khaja, Tanweer Hussain, Jaanus Remme, Umesh Varshney
Summary: The study demonstrates that the L48K mutation in uS12 leads to a cold-sensitive phenotype and ribosome biogenesis defect in E. coli, affecting initiation and elongation translation steps, and interacting genetically with RRF and Pth, revealing a novel role of the PNSA loop in ribosome recycling.
MOLECULAR MICROBIOLOGY
(2021)
Article
Developmental Biology
Anupama Rao, Baken Lyu, Ishrat Jahan, Anna Lubertozzi, Gao Zhou, Frank Tedeschi, Eckhard Jankowsky, Junsu Kang, Bryan Carstens, Kenneth D. Poss, Kedryn Baskin, Joseph Aaron Goldman
Summary: The eIF4E family of translation initiation factors is important for heart development and regeneration, particularly the Eif4e1c family. Deletion of Eif4e1c in zebrafish causes growth deficits and impaired proliferative responses to cardiac injury. Ribosome profiling also reveals changes in translation efficiency of genes known to regulate cardiomyocyte proliferation.
Article
Biochemistry & Molecular Biology
Zainab Fakih, Melodie B. Plourde, Charlene Eugenie Tomi Nkouankou, Victor Fourcassie, Sylvie Bourassa, Arnaud Droit, Hugo Germain
Summary: Plants have developed strategies to cope with various stresses, and ribosomes can adapt to different stress conditions. By analyzing immunopurified ribosomes from Arabidopsis leaves treated with an inducer of plant innate immunity, potential ribosome-associated proteins involved in innate immunity were identified.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alfredo Berzal-Herranz, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, Cristina Romero-Lopez
Summary: This study provides evidence that West Nile virus promotes a cap-independent translation initiation mechanism in mammalian and insect cells, and suggests that its 3' UTR is involved in fine-tuned translation regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Dentistry, Oral Surgery & Medicine
G. Li, Q. Li, Z. Shen, X. Lin, X. Li, J. Wang, B. Zhao, Y. Feng, L. Feng, W. Guo, L. Hu, J. Wang, C. Zhang, Z. Fan, S. Wang, X. Wu
Summary: The successional dental lamina (SDL) of permanent teeth is maintained in a quiescent state until adolescence. Biomechanical stress generated by the rapid growth of deciduous teeth inhibits SDL development. A specific fibroblast subtype, DFDP, in the dental follicle mesenchyme was identified, which is related to biomechanical stress and plays a role in maintaining SDL niche homeostasis. The biomechanical stress-mediated RUNX2-fibulin-1 axis inhibits SDL initiation.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Chemistry, Medicinal
Irina Dobrescu, Elie Hammam, Jerzy M. Dziekan, Aurelie Claes, Ludovic Halby, Peter Preiser, Zbynek Bozdech, Paola B. Arimondo, Artur Scherf, Flore Nardella
Summary: Malaria drug resistance poses a challenge in treating the deadliest parasitic disease affecting millions worldwide. However, the development of quinoline-quinazoline-based inhibitors (compound 70) shows promise as new antimalarials. Through thermal proteome profiling (TPP), researchers discovered that eukaryotic translation initiation factor 3 (EIF3i) subunit I is the main target protein stabilized by compound 70 in Plasmodium falciparum. Further studies on PfEIF3i could lead to the design of new antimalarial drugs targeting the parasite's entire life cycle.
ACS INFECTIOUS DISEASES
(2023)
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.
Article
Biochemistry & Molecular Biology
Jitendra Singh, Rishi Kumar Mishra, Shreya Ahana Ayyub, Tanweer Hussain, Umesh Varshney
Summary: This study reveals the crucial role of the interaction between the N-terminal domain (NTD) of initiation factor 3 (IF3) and initiator tRNA (i-tRNA) in bacterial translation initiation and growth fitness of Escherichia coli. Specific mutations in NTD disrupt its interaction with i-tRNA, leading to impaired translation fidelity and bacterial growth.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Eric Huntzinger, Jordan Sinteff, Bastien Morlet, Bertrand Seraphin
Summary: Proteins with RNB domain are present across various species, and a new RNB protein, HELZ2, was identified in humans. HELZ2 protein in humans is produced from an unexpected non-canonical initiation codon and can function as an active ribonuclease despite a key residue substitution. The activity of HELZ2 as a ribonuclease is lost in cancer cells due to somatic mutations. HELZ2 also contains RNA helicase domains and zinc fingers, and its expression is induced by interferon treatment. It is involved in degrading structured RNAs through ATP-dependent displacement mediated by its RNA helicase domains and ribonucleolytic action.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yan Zhang, YanKun Chen, JianPing Zhou, DaQian Sun, HongMei Li
Summary: This study achieved the connection between TC4 Titanium alloy and Al2O3 ceramic by laser welding, forming fusion weld and brazed weld. The brazed weld at the Ti-ceramic interface exhibited specific microstructures, leading to the fracture of the joint.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ramy Kazan, Gabrielle Bourgeois, Christine Lazennec-Schurdevin, Eric Larquet, Yves Mechulam, Pierre-Damien Coureux, Emmanuelle Schmitt
Summary: This study investigates the late steps of translation initiation in Pyrococcus abyssi and reveals that aIF5B bound to GTP accelerates subunit joining without GTP hydrolysis. Crystal structures and cryo-EM analysis demonstrate the cooperative role of archaeal 5B and 1A factors in promoting a conformation of the initiator tRNA favorable to subunit joining.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Ipsita Basu, Biswajit Gorai, Thyageshwar Chandran, Prabal K. Maiti, Tanweer Hussain
Summary: Accurate and high-speed scanning and selection of the correct start codon are important events in protein synthesis. Molecular dynamics simulations and energy calculations suggest that the ribosomal 48S pre-initiation complex (PIC) may reject most non-AUG codons, with initiation factor eIF1 playing a crucial role. This study provides insights into the scanning process and the involvement of initiation factors in codon-anticodon-ribosome network stability.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jiangning Wang, Kelvin Caban, Ruben L. Gonzalez
JOURNAL OF MOLECULAR BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Kelvin Caban, Michael Pavlov, Mans Ehrenberg, Ruben L. Gonzalez
NATURE COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Rachel C. Fleisher, Virginia W. Cornish, Ruben L. Gonzalez
Article
Biochemistry & Molecular Biology
Solomon A. Haizel, Usha Bhardwaj, Ruben L. Gonzalez, Somdeb Mitra, Dixie J. Goss
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Bijoy J. Desai, Ruben L. Gonzalez
NATURE CHEMICAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Simon Diez, Jaewook Ryu, Kelvin Caban, Ruben L. Gonzalez, Jonathan Dworkin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Benjamin D. Hobson, Linghao Kong, Erik W. Hartwick, Ruben L. Gonzalez, Peter A. Sims
Article
Biology
Eric D. Hoffer, Samuel Hong, S. Sunita, Tatsuya Maehigashi, Ruben L. Gonzalez, Paul C. Whitford, Christine M. Dunham
Article
Multidisciplinary Sciences
Howard Gamper, Haixing Li, Isao Masuda, D. Miklos Robkis, Thomas Christian, Adam B. Conn, Gregor Blaha, E. James Petersson, Ruben L. Gonzalez, Ya-Ming Hou
Summary: The study investigates the translation of quadruplet codons by a +1-frameshifting tRNA SufB2, revealing that SufB2 initially uses triplet anticodon-codon pairing in the 0-frame to decode the quadruplet codon before shifting to the +1-frame during tRNA-mRNA translocation. The frameshifting mechanism of SufB2 involves perturbation of a crucial ribosome conformational change, highlighting the potential for engineering specific ribosome conformational changes to enhance genome recoding efficiency.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Korak Kumar Ray, Anjali R. Verma, Ruben L. Gonzalez, Colin D. Kinz-Thompson
Summary: A critical step in data analysis is to identify features with theoretically defined shapes in N-dimensional datasets. This study presents a probabilistic solution using Bayes' rule to calculate the probability of data having specific shapes. The approach can objectively compare different theories, identify changes between datasets, and detect features within data using Bayesian Inference-based Template Search.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Asem Hassan, Sandra Byju, Frederico Campos Freitas, Claude Roc, Nisaa Pender, Kien Nguyen, Evelyn M. Kimbrough, Jacob M. Mattingly, Ruben L. Gonzalez, Ronaldo Junio de Oliveira, Christine M. Dunham, Paul C. Whitford
Summary: Protein synthesis requires large-scale rearrangements of the ribosome. By analyzing the RCSB PDB database, we describe the structures of ribosome complexes and subunits from various species. We found universal and organism/domain-specific aspects of subunit rearrangements. This study provides a foundation for further research on the dynamics of this molecular machine.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Korak Kumar Ray, Colin D. Kinz-Thompson, Jingyi Fei, Bin Wang, Qiao Lin, Ruben L. Gonzalez
Summary: Biomolecular machines utilize thermal and chemical energy to perform cellular processes, and they require dynamic rearrangements of structural components. The physical and structural mechanisms through which ligands achieve repurposing of these dynamics remain unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)