Article
Biochemistry & Molecular Biology
Alice Romagnoli, Paolo Moretti, Mattia D'Agostino, Jesmina Rexha, Nunzio Perta, Astra Piccinini, Daniele Di Marino, Francesco Spinozzi, Anna La Teana
Summary: Researchers have conducted a structural and functional analysis of aIF5A in the crenarchaeal Sulfolobus solfataricus model organism, and found that it is associated with multiple RNA molecules and possesses specific ribonuclease activity. The study also revealed that aIF5A can exist in two conformations, with the monomeric form more likely to associate with RNA. Modeling the three-dimensional structure of S. solfataricus aIF5A showed that it has an extended positively charged surface, which may explain its strong tendency to bind to RNA in vivo.
Article
Biochemistry & Molecular Biology
Zuben P. Brown, Irina S. Abaeva, Swastik De, Christopher U. T. Hellen, Tatyana Pestova, Joachim Frank
Summary: This study presents cryo-EM structures of hepatitis C virus IRES initiation complexes, revealing the dynamic network of 40S/IRES contacts and the conformational changes during the transition from eIF2- to eIF5B-containing 48S complexes, providing important insights into the process of subunit joining.
Article
Microbiology
Zhaolan Ding, Teresa M. Lamb, Ahmad Boukhris, Rachel Porter, Deborah Bell-Pedersen
Summary: In the model fungus Neurospora crassa, the circadian clock regulates rhythmic protein synthesis by controlling the phosphorylation and dephosphorylation of a conserved translation initiation factor, eIF2 alpha. This temporal coordination of phosphorylation and dephosphorylation events allows for the partitioning of translation to the night, which helps coordinate energy metabolism with protein synthesis and cellular growth.
Article
Biology
Faisal Alharbi, Thomas Knura, Bettina Siebers, Kesen Ma
Summary: This study investigates the thermostability and oxygen stability of pyruvate decarboxylase (PDC) from two thermoacidophile microorganisms, Saccharolobus solfataricus and Sulfolobus acidocaldarius. The results show that both enzymes are CoA-dependent and thermostable, with no loss of activity in the presence of oxygen.
Article
Biochemistry & Molecular Biology
Oleg S. Nikonov, Natalia A. Nevskaya, Maria B. Garber, Stanislav Nikonov
Summary: This study conducted a comparative analysis of the structures of aIF2 beta and gamma subunits in archaea and eukaryotes, revealing differences in the environments and functions of their Cys2-Cys2 motifs in crystals.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Microbiology
Giada Lo Gullo, Maria Luisa De Santis, Alessandro Paiardini, Serena Rosignoli, Alice Romagnoli, Anna La Teana, Paola Londei, Dario Benelli
Summary: IF6 translation factor is a protein shared by Archaea and Eukarya, but not present in Bacteria. Its function is to prevent ribosome association by binding to the large subunit. In Eukarya, the release of IF6 from the ribosome requires the action of GTPase Efl1 and docking protein SBDS, while Archaea lack a homolog of Efl1 but have a homolog of SBDS. The release of IF6 in Archaea involves GTPase activity of aEF-2 and is inhibited by the presence of aSBDS, with a mechanistic interplay between aIF6, aSBDS, and aEF2 on the ribosome surface.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Rikako Shishiuchi, Hyejin Kang, Takayoshi Tagami, Yoshitaka Ueda, Weeranuch Lang, Atsuo Kimura, Masayuki Okuyama
Summary: This study identified two α-L-glucosidases derived from Cecernbia lonarensis LW9 and confirmed the existence of α-L-glucosides in nature. These enzymes selectively hydrolyze α-L-glucosides and can also synthesize α-L-glucosidic linkages through transglucosylation activity. This research will contribute to further investigation on the physiological effects of α-L-glucosides in humans and the discovery of novel α-L-glucoside-related enzymes.
Article
Biochemistry & Molecular Biology
Alka Rao, Niels A. W. de Kok, Arnold J. M. Driessen
Summary: Cellular membranes play essential roles in compartmentalization, permeability maintenance, and fluidity in all three domains of life. Archaea, as the third domain of life, have unique phospholipid compositions. The study focuses on Sulfolobus acidocaldarius, an archaeon with a membrane dominated by glycerol dialkyl glycerol tetraethers (GDGTs), and the effects of the antifungal terbinafine on its lipidome and transcriptome. The results show that terbinafine treatment leads to growth phase-dependent depletion of GDGTs and the accumulation of bilayer-forming dialkyl glycerol diethers (DGDs). Transcriptomic analysis reveals significant differential expression of genes involved in respiratory stress, isoprenoid biosynthesis, and saturation. Overall, terbinafine inhibition affects the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization in S. acidocaldarius.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nicola Curci, Andrea Strazzulli, Roberta Iacono, Federica De Lise, Luisa Maurelli, Mauro Di Fenza, Beatrice Cobucci-Ponzano, Marco Moracci
Summary: Hemicellulases from hyperthermophilic archaea show promising potential as biocatalysts for the efficient hydrolysis of plant biomasses, particularly due to their stability in harsh conditions. Despite being less studied compared to bacterial counterparts, these enzymes demonstrate efficient monosaccharide release in the hydrolysis of xyloglucan oligosaccharides, indicating their valuable industrial applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Mauricio M. Oliveira, Eric Klann
Summary: This review discusses the requirement of de novo protein synthesis in memory formation and its mechanisms. It also introduces the regulation of local dendritic and axonal translation and its impact on memory consolidation. The review emphasizes the importance of eIF2α-dependent translation initiation in synaptic plasticity and memory formation, and explores the role of aberrant eIF2α phosphorylation in Alzheimer's disease.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Physical
Sylvain F. Royer, Xuan Gao, Robin R. Groleau, Marc W. van der Kamp, Steven D. Bull, Michael J. Danson, Susan J. Crennell
Summary: This study describes the creation of two new mutants of a hyperthermophilic aldolase, which can catalyze aldol reactions between pyruvate and non-natural L-glyceraldehyde to enable the diastereoselective synthesis of L-KDGlc and L-KDGal. High-resolution crystal structures of these mutant aldolases have been analyzed to understand the molecular mechanism underlying the changes in diastereoselectivities observed in these variant-catalyzed aldol reactions.
Article
Microbiology
Alejandra Recalde, Marleen van Wolferen, Shamphavi Sivabalasarma, Sonja-Verena Albers, Claudio A. Navarro, Carlos A. Jerez
Summary: The study revealed that polyphosphates might play a role in regulating biofilm formation and related processes in archaea, as the absence of polyP led to reduced biofilm formation and motility in the strains. This provides new insights into biofilm formation in archaea.
Article
Microbiology
Peter B. Bohall, Stephen D. Bell
Summary: The loss of putative repair polymerases PolB2 and/or PolB3 in the crenarchaeon Sulfolobus islandicus leads to a modest growth advantage and insensitivity to hydrogen peroxide. However, cells lacking PolB3 show enhanced sensitivity to the DNA damaging agent 4-NQO, suggesting that these non-essential DNA polymerases may influence DNA repair pathway choice in hyperthermophilic aerobes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ronald C. Wek, Tracy G. Anthony, Kirk A. Staschke
Summary: Organisms adapt to changing environments by engaging cellular stress response pathways, such as the integrated stress response (ISR). This review focuses on the mechanisms of eIF2 alpha kinases as first responders of stress, the regulation of eIF2 alpha phosphorylation and other stress signals, and the differential mRNA translation triggered by the ISR. It also discusses the synergy between the ISR and mTORC1 in amino acid insufficiency, as well as the pathological conditions and therapeutic strategies related to aberrant regulation of the ISR.
ANTIOXIDANTS & REDOX SIGNALING
(2023)
Article
Cell Biology
Simon Lizarazo, Yeeun Yook, Nien-Pei Tsai
Summary: Alzheimer's disease is a common form of dementia, characterized by the accumulation of amyloid beta peptide. This study reveals that Fmr1 is involved in A beta-induced translational suppression, leading to hyposynchrony of neuronal firing activity and loss of excitatory synapses. The mechanism involves the repression of phosphatases by Fmr1, resulting in translational suppression.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Microbiology
Attilio Fabbretti, Cheng-Guang He, Eleonora Gaspari, Sonia Maffioli, Letizia Brandi, Roberto Spurio, Margherita Sosio, Daniela Jabes, Stefano Donadio
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2015)
Article
Biochemistry & Molecular Biology
Tatsuya Kaminishi, Andreas Schedlbauer, Attilio Fabbretti, Letizia Brandi, Borja Ochoa-Lizarralde, Cheng-Guang He, Pohl Milon, Sean R. Connell, Claudio O. Gualerzi, Paola Fucini
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biochemistry & Molecular Biology
Jorge P. Lopez-Alonso, Attilio Fabbretti, Tatsuya Kaminishi, Idoia Iturrioz, Letizia Brandi, David Gil-Carton, Claudio O. Gualerzi, Paola Fucini, Sean R. Connell
NUCLEIC ACIDS RESEARCH
(2017)
Article
Multidisciplinary Sciences
Attilio Fabbretti, Andreas Schedlbauer, Letizia Brandi, Tatsuya Kaminishi, Anna Maria Giuliodori, Raffaella Garofalo, Borja Ochoa-Lizarralde, Chie Takemoto, Shigeyuki Yokoyama, Sean R. Connell, Claudio O. Gualerzi, Paola Fucini
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biotechnology & Applied Microbiology
Naser Aliye, Attilio Fabbretti, Giulio Lupidi, Tsepo Tsekoa, Roberto Spurio
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Ulisse Ulissi, Attilio Fabbretti, Marco Sette, Anna Maria Giuliodori, Roberto Spurio
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Anna Maria Giuliodori, Anna Brandi, Shivaram Kotla, Francesco Perrozzi, Roberto Gunnella, Luca Ottaviano, Roberto Spurio, Attilio Fabbretti
Article
Biochemistry & Molecular Biology
Anna Maria Giuliodori, Attilio Fabbretti, Claudio Gualerzi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Microbiology
Attilio Fabbretti, Retina Capuni, Anna Maria Giuliodori, Lucia Cimarelli, Antonino Miano, Valerio Napolioni, Anna La Teana, Roberto Spurio
Article
Biochemistry & Molecular Biology
Jose A. Nakamoto, Wilfredo Evangelista, Daria S. Vinogradova, Andrey L. Konevega, Roberto Spurio, Attilio Fabbretti, Pohl Milon
Summary: Initiation factor IF3 is crucial for accurate and fast bacterial mRNA translation initiation. The interplay between IF3 domains is dynamic and responsive to the binding of 30S ligands. IF1 and IF2 play a role in compacting IF3 structure, while IF3N and IF3C are involved in binding different proteins and tRNAs to ensure accurate translation initiation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Rossana Petrilli, Attilio Fabbretti, Alex Cerretani, Kathleen Pucci, Graziella Pagliaretta, Matteo Picciolini, Valerio Napolioni, Maurizio Falconi
Summary: The production of leachate, a liquid formed by rainwater percolation through waste, has led to serious problems in municipal wastewater treatment plants due to its high levels of toxic ammonia. In this study, a metagenomic approach based on next-generation sequencing was used to analyze the microbial composition of sludge in a wastewater treatment plant in Italy. Through enrichment experiments, a minimal bacterial community capable of degrading high concentrations of ammonium in leachate was identified. Further analysis revealed that certain bacterial families were responsible for ammonia oxidation and three bacteria genera were capable of nitrification coupled with denitrification. These findings provide a foundation for optimizing microorganism mixtures for the biological removal of ammonia in leachate.
Article
Microbiology
Valerio Napolioni, Lucia Cimarelli, Antonino Miano, Anna La Teana, Retina Capuni, Anna Maria Giuliodori, Attilio Fabbretti, Roberto Spurio
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2019)
Article
Infectious Diseases
Roberto Chulluncuy, Carlos Espiche, Jose Alberto Nakamoto, Attilio Fabbretti, Pohl Milon
Meeting Abstract
Biochemistry & Molecular Biology
M. Duval, A. Korepanov, O. Fuchsbauer, P. Fechter, A. Haller, A. Fabbretti, L. Choulier, R. Micura, B. Klaholz, P. Romby, M. Springer, S. Marzi
Review
Chemistry, Medicinal
Anna Maria Giuliodori, Roberto Spurio, Pohl Milon, Attilio Fabbretti
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2018)